Okay, first off--since you guys are still very new to all of this--you need to read the sticky thread carefully:
http://www.canadavisa.com/canada-immigration-discussion-board/spousal-sponsorship-t46995.0.html.
1) As explained in that link above, yes you most certainly can apply outland even if your wife is visiting with you in Canada. Note the terminology, it's important especially when dealing with CIC and approaching your applications: she is not permitted to officially MOVE to Canada with you until she's a PR. Until she gets her PR status, she's a visitor. You'll also need to be mindful about maintaining her status while she is here waiting out the PR process with you.
2) The best advice anyone can give you about the application forms: read the instructions. Over and over again. Past that, any questions specific to your own situation (or about parts of the form that just don't seem clear to you), definitely feel free to ask about here and people will be able to help out.
3) All the forms you'll need for outland:
http://www.cic.gc.ca/english/information/applications/fc.asp. It's all broken down there for you. Note the US specific region guide near the end.
4) Follow the document checklist in the US region guide. Yes she needs to get her medical done before you submit your application; proof of the medical is one of the required documents in the checklist. When she gets the medical done, her DMP should give her copy 2 of Medical Report Section A. This is what she'll need to send with the application.
5) About her FBI certificate. That will need to be no more than 3 months old by the time it's received by CIC. Just something to be aware of, because for many people it can take months just to gather all the necessary documentation needed to submit with the application itself.
You have a lot of reading ahead of you, but it's important not to skim over any instructions or the checklist itself. It all seems extremely overwhelming at first, but it's not as bad as it looks. And at least in my case, I've found a lot of my questions answered just by doing a search of the threads in this forum. Hopefully that's enough to get you started, and others may chime in later with further advice. Good luck.