To be perfectly honest, although you're supposed to be able to run a scan on a PC and work on it at the same time, realistically your PC is going to chug along like your granny unless you've got a dual core processor (or above).
But on my desktop, for example, I've got the old style processor and running a spyware scan and trying to run other applications at the same time just doesn't work. But on my laptop, which is a dual core Vista PC, I can run a spyware scan and any other programs easily at the same time.
If your PC isn't the latest model then you've really got two choices here.
Option 1: Leave the PC on over lunch / while you watch TV / at the end of the day and run the full scan then.
Option 2: If you have your PC on all of the time, or it starts up at certain times, then running the scheduler is a great way to keep all the spyware junk off your PC.
How to run a scheduled scan in STOPzilla

1) Double click on the STOPzilla icon in the system tray.
2) Click on Scheduler in the left menu.
(If you've not set anything up here, it will say 'There are no scans currently available')
3) Next up, click on Settings.
4) In the Perform: box, click on the kind of scan you want. The obvious choice here I'd recommend is 'Full'.
5) You can then set either a daily or weekly scan here and it's pretty self explanatory from here on. Just choose a day and a time.
If you're anything like me, running a manual scan will just never happen because there's frankly more important (and interesting) things to do with your time. So it's a good idea to set up scheduling if you can.