It is no dumb question IMO... (there is no such thing as dumb question anyway 
Also struggling with this. I am working on 2 sketches simultaneously for 2 arduinos communicating thru I2C. Switching from one to the other is just a pain.
I have to
- swap the sketch (did not find any efficient way)
- change the COM port
- and possibly changing the board type
I often end up uploading the sketch to the wrong arduino or compile for the wrong board 
I'll try the multiple workspaces trick.
May be also the multi root workspace would be helpful.
JS