OK, first of all, she is not in Canada legally at this point so you do not want to risk sending in an application to sponsor via the inland process simply because of the promise of an Open Work Permit. She has, essentially, lost her option for being able to get an OWP anytime soon because of her overstay. If you apply inland, it could literally be
years before she gets an OWP, much less permanent status.
She does
not have to leave Canada to be eligible to apply via the
outland PR process - with the application going first to CPC-Mississauga (where they assess you as her sponsor) and then to Buffalo for her assessment. Buffalo is finalizing spousal applications within 11 months - and your assessment at CPC-M should take about a month. If you provide a complete, straight-forward application that includes - upfront - both her proof of medical examination (which can be done in Canada) and an FBI clearance (which can be ordered from and sent back to Canada), you can expect processing to be finalized in less than the year they quote. Applying outland protects both your right to appeal a refusal, and protects her ability to leave Canada (if she has to) without it affecting the processing of the outland application. If she leaves Canada with an inland PR ap in process, it fails unless she can get back into the country - and there is never any guarantee of that, especially since she has a significant overstay.
Here is the best way for the two of you to handle this: prepare and submit an outland PR package using a residential address in the US for her (can be a family member's address) and a mailing address in Canada. Track the mailing of the application to CPC-M and get delivery confirmation. Once you have your sponsorship approval letter (about 6 weeks after receipt) the two of you should leave Canada together and spend a week or so in the States. When coming back to Canada together, carry with you a certified copy of your marriage licence, a copy of the letter you will get from your employer to submit with the PR ap regarding your length of employment and salary, and your sponsorship approval letter. When you approach the border
you tell the officer that this is your US citizen wife, that you have applied to sponsor her for permanent status and would like permission for her to stay with you in Canada while awaiting finalization of her application. Do NOT get into how she has been with you in Canada and then you went to the States and now you're coming back. They will assume she has been somewhere other than Canada since you got married - unless you give them information to the contrary, they will give her the benefit of the doubt on your account. Assuming all your paperwork (and her passport) are in order, they should document her on a Visitor Record, which gives her temporary status to remain in Canada for a specific period of time, and the ability to
apply to extend that status (based on the PR ap in process) if it is not finalized before her VR expires. The VR will not allow her to work in Canada, but processing on the outland PR ap will be finished long before she would even have first stage approval (and an OWP) through the inland process - even if it wasn't for her overstay.
There is more information on how this all works on the
US2Canada website - under the Visiting tab, read through and go to Visitor Record for complete instructions.