Dark,

Squatting three times a week is fine for most people at your level. SS is for novices, and since you're a novice, it'll probably be fine for you (if you weren't a novice, you wouldn't be doing this program). If you find youself fried or sluggish or whatever, squatting at 70% of your Monday work weight on Wednesdays is an option.

As Riddick pointed out, waiting until you're not sore anymore to train again is a great way to guarantee being sore every time. Soreness says more about your conditioning than anything. Your first couple of weeks might leave you sore, but you'll adapt and be fine. As long as you're not crippled, work through it. Only worry if your performance is way down.

Cheers,
Jeff