No need to apologize for being a newb! We've all been there. Ok, there's two basic schools of thought on your dilema:
1) Mask off the cockpit area, paint your model, paint the canopy separately and attach afterwards
2) Attach the canopy, mask, and paint the model
Now, I tend to do a hybrid of the two, depending on the canopy shape. Sometimes I'll take #2, but others I mask and then attach, then paint. I feel like this gives me a chance to address any fit issues on the canopy to plane bond. Sometimes canopies fit great and don't need any fiddling, other times that joint needs a lot of attention.
If I was in your shoes, I would do as much masking as I could off the model, attach, and paint. An aside, I mask my canopies by cutting thin strips of masking tape and outlining the frames, followed by bigger pieces to fill the gaps. Also, before you paint the final color, maybe try to paint the interior color on the canopy first, then the topcoat over that. That way, the interior color can be seen inside the canopy, but it's painted on the outside! It adds a bit of reality to the kit.
Wow, sorry for the information overload there, jburns! I hope some of that helped! Don't forget to post photos in the Aircraft Section! I'd love to see this plane (I live 15 minutes from Port Columbus!).