to set up a runtime folder.... i do this with mine... i just made a folder for whatever project i'm working on in my documents... inside the project folder i created the apropriate folders..... 

1. create a folder labeled "runtime"

2)inside that make 3 separate folders "geometries", "libraries" (inside this folder you will also need to create a folder titled "character"), and "textures"

the libraries folder must have a folder labeled Character inside (this is where you put the folder in the next step and where your finished cr2 will be saved to and it absolutely must be set up this way if you want the new cr2 to work)

3)  create a folder with the name of your project as it will appear as if a finished item for download (ie bob's robot thingy) and copy it  so that each folder ("geometries", "libraries" > "character", etc) has a copy of this new folder in it.

4. copy (or save) your obj. file into the folder (ie bob's robot thingy) inside the geometries folder

5. cr2 gets saved in the folder in runtime>libraries > character > (bob's robot thingy for example)

6. textures and uv maps get saved in the internal folder you created inside the runtime>textures>(ie bob's robot thingy) folder

this full runtime set-up can be stored anywhere on your comp... but for the items and cr2's to work the basic structure within the runtime folder must be maintained...