I would suggest to use for each project its own workspace. It does not make sense to mix different project within one TS workspace - b/c they are different, and will not be deployed together (although you can use shared code modules/subsequence between them, but this is a bit another topic). And I agree with 2Shanez, that workspace - is quite nice for deployment preparation, b/c it links all the needed are required files together.
But once you've created deployed image once, you can reuse TestStand Deployment configuration file (*tsd), which will contain all the needed settings for deployment.
Thus, you can use one workspace with multiple projects, and prepare deployment for each of them (b/c at the end you just need to be carefull with selecting of what VIs/sequences will be deployed, and their folder structure, etc.), and for each of them save tsd file. And, afterwards, do updates of deployment already not based on workspace file, but based on tsd-file.