I am doing a lot of physics on Mathematica and am running into questions regarding the software. Are these ok to ask in the main section? Anywhere where they might be more appropriate?
No, use https://mathematica.stackexchange.com/ (which was launched in 2012) instead.
Note there is also Mathematica proposal on Area. Yet in a very early stage.
No, questions on Mathematica in general aren't really appropriate for this site because Mathematica is just a tool used to do physics. I'd suggest going to Super User, or if what you're trying to do with Mathematica is complex enough to qualify as programming, Stack Overflow. That being said, there are a few Mathematica-related questions that would be appropriate here, because they are actually about the physics that motivates the calculation.
If you like, you can bring this up in the chat room and someone can advise you on the best place to send your question.