Sponsoring American Spouse w/ Work Permit

Hi there, I posted here a while back about potentially marrying my girlfriend in the spring. Well, happy to say that we are now engaged with a May 22 wedding coming up. I have a fairly basic question to help me get the process started.

We are currently in the process of getting her a Work Permit. She has been given a job offer and the employer just has to get the LMO approved. Because she will have temporary resident status (assuming it gets approved), should we apply as "In Canada" rather than "Outside Canada"? Here's the tricky part. Even though she will have a work permit and temporary resident status, she will need to go back to the States in the fall to finish up school. So while we will both be in Canada for a while, she will be outside the country (other than for some visits) later while she finishes school, but at the same time will likely still have a valid work permit. OR... Since she will be graduating as an RN I am wondering if we should just wait until then and look into the Skilled Workers app.

Thoughts?