Another way to do it is to install the portable version multiple times on different folders.
As an example:
c:\program files\MtgStudio
c:\program files\\MtgStudio_MTGO
c:\program files\\MtgStudio_Trade
...
I put the "card art" into
c:\program files\MtgStudio and set up the configuration of
c:\program files\\MtgStudio_MTGO to look into
c:\program files\\MtgStudio\cart art instead of its default one. This way, I do not need to copy image files multiple times. You can probably delete the "My decks" directories in all but one installation folders as well.
You just have to create shortcuts to the differents .EXE files et voilà. You have different collections without the need to rename/delete/...
Apparently, you are not able to run multiple instance of MTG Studio at once, but maybe there is a flag somewhere to allow it. I didn't search for it

Anyway, I have a question: why don't you filter you collection with F3 (upper grid) or shift-F3 (for the lower grid) instead of creating multiple files (per collection) ?