You can have as many versions as you like installed so I wouldn't worry about that.
Just make sure you backup your memory card files.
Okay, how? What do I overwrite/not overwrite?
I just have different versions installed in separate folders. I also remove the "portable.ini" before launching. Your memory card files are stored in Documents/PCSX2/memcards. Back those up to a folder of your choice. I haven't had any issues with my memory cards switching between 1.4.0 and the latest GIT builds, but YMMV. Back them up to be safe.