It's a little work, but I have a separate domain I use for testing sites, and have several installations of Zencart on it now. A subdirectory of your current domain would be fine, too. If I want to test a mod, I install it on one of those, and try it out. If it seems to work OK, then it goes on the live site.

The main issue with multiple mods is the possibility that two mods will change the same file, so when you install the second mod, it overwrites that file (or those files) and your store can be broken. I don't know an easy way to prevent that. The way I do it is by having a folder on my local computer named after each site I have, with subfolders containing the mods I have installed. If I want to install a new mod, I manually check the files it contains against the ones I have installed already, merging if necessary.

It's a certain amount of work, but it also serves to help keep mods to a minimum, which I think is a good thing.