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Ive been shooting recently with two cameras and I wonder how can I change folder name on 6D so I can have both cameras files on separate folders in the same card. Or is this even possible in-camera? I cant find it anywhere on the menu.

Do you intend to move the same card from one camera to the other?
It's not too smart, since each time you insert a card with images on it in the camera, the camera will start the indexing procedure, and if there are quite a few images, this process takes a long time to complete.
But all cameras allow the creation of a new folder, so the 6D does that too. Then some cameras allow you to choose which folder to use, not just the most recently created. The 7D supports this, so I presume the 6D does too, but I haven't checked.
You can probably set different file names for the cameras too (the 7D supports it, at least), so that pictures taken will not be called IMG_0123, IMG_0124 etc., but A6D_0123 from one camera and B6D_0124 from the other, for example.
Significantly smarter and easier is using one card in each camera, and then decide at upload time how you want to store the images in your computer. Together, separated or whatever.

My intention was to copy files from camera to my laptop for storage until I come back from my trip (I go photograph brown bears soon for a 4 day trip) if camera could rename folder it would be easier for me to keep things organised until I can place them to my hard drive.
But still cant find it in the menu? Can some one tell me how to do it step-by-step?
I can create new folder but cant rename it, its just 100CANON or 101CANON etc.
Can I change this for example: 101CANON-6D etc. or to change filename. But how?

Why not use the EOS Utility to accomplish the transfer? The software sets up a folder structure based on date using a format of yyyy-mm-dd.
The points made by 'apersson850' are important, so you should carefully review them and the ramifications. Beyond that review pages 160 and 161 of the manual for the procedure to set up and use a specific folder.

With EOS Utility you can set it up to rename the files in just about any way you like, when doing the transfer. Easy to program different handling for files from different cameras, or moving the files to different folders on the laptop. That would accomplish the same thing.
How do yo intend to transfer the images? By cable or by moving the card? Even if you move the card you can easily lift the images to different destination folders, to keep them separated.

You can create names for folders(according to the prescribed theme: ###ABC_D), but only using a computer to do so. However the card can then be placed in and used in the camera afterward. According to the manual:

Adobe pdf pack download for mac. SD cards are the cheapest things you put in your camera, just keep the card in camera. It really makes no sense to move cards between cameras and in fact, Canon recommends formatting a card that has been used in a difference camera (although I know you can do it)
What are you trying to accomplish by only using one card?

So have we concluded that 6D can not do this in camera?
1Ds can, and so can 5DIII. Not sure about 6D.

The OP can change any of the folders to dates or names using the EOS software used to download the photos to the computer, or with any of the Adobe photo downloaders. The name (or date) can be changed just before downloading the photos.
He should also be able to change the folder name or date once the photos are downloaded to the computer. I don't know how to do this on a PC, but on the Mac all you have to do is to select the folder's name or date (with the mouse's button to insert the text tool or cursor), and then type whatever you want.

My 5DC body has a 'Select folder' menu choice if you scroll down (you can also use it to create a new folder), it's below the 'File numbering' menu item. But, my 30D doesn't have this function. I don't know what newer cameras have it! The problem with creating a folder in the computer is that if the camera does not have a 'select folder' function then, well, you can't do it!
For what I do, I don't 'share' cards between cameras. If I do switch a card over, I'll Format it in the camera to make sure that everything is 'compatible', but doing so would erase files from another camera. I pack spare cards, so I don't have to bother with that (among other things)!

Maybe I'm confused, but are you using one card for both cameras? If so, why? Why not have a card for each, then you can download each to a different folder on the computer.
I can't imagine anything that would make me swap one card between cameras unless all but one card failed while I was out of touch with anyplace to buy a new one. I generally carry at least 4 cards, and I only have one body. For my 17 day trip to Africa this fall I plan on having at least 6 cards with me, and plan on changing them every couple of days so that if anything fails, I only lose 2 or 3 days worth of shooting (I can't download anything while on the trip as weight limitations don't allow taking my laptop with me).

I do use individual cards for each camera. I have 7 cards now and last time they were full in 2 days. Triedto create folders in my laptop to the card, didnt work. 6D still makes folder called 100CANON and places images there.
Point of having diffrent filenames / folders is because I am going to empty my memory cards to the laptop while shooting at the same time. I dont have time to rename them all the time on my laptop.

To be honest, I can't imagine anything that would make me be on top of keeping track enough to know one way or the other.
I have several bodies and dozens of cards. It would never occur to me to try and keep them segregated to specific bodies.

I wasn't meaning that you never use a card for a different camera body, only that you remove the images and reformat before doing so. The way the OP was stated, it really sounded like he was thinking of using one card between two bodies during a single shoot without downloading the photos. That was the only reason I could think of for his needing to change the folder name in camera. Otherwise you just download the images to a folder you create and name on your computer, so why does the folder have to be named anything in particular on the camera. I don't download the folder from the camera, only the photos. I still don't know what the OP is getting at.

I have folders with different names on my card, and select a certain folder prior to shooting. Provided I remember, that is.
Since I sometimes use my camera for things at work, I have a folder for that. It makes it a lot easier to locate shots related to work, taken in between shots related to completely different things. But it's not to distinguish between different hardware, but between different file content.