I think you can call the port you entered and they will give you instructions on how to apply for your entry record. That's what i did when my passport didn't get stamped at Maine-New Brunswick border. I think it took me about a month to get that entry record letter. But I didn't end up using that letter because I didn't end up submitting the application at that time. When I did submit my application, I didn't have a stamp on my passport again (Montreal airport custom didn't stamp it). So I just included a letter with my application saying that my passport didn't get stamped and I attached my flight tickets to that letter. I guess they were ok with that since I didn't get any other request from them regarding the stamp.
My case was very similar to yours, by the way. American citizen with Canadian husband. I applied outland and stayed in Canada as a visitor throughout the whole process. I had to extend my visitor status once. I could have left and reentered but I was afraid of being denied at reentry. Some people had to extend their visitor status twice. It all depends on how long you have been in Canada when you submit your application and how long your application process takes.
Outland is highly recommended by all the seniors on this forum to Americans with straight forward application. I took their suggestions and it worked out for me. A year ago I was ready to send off my inland application when I stumbled upon inland vs outland discussion. I changed my mind and applied outland instead.
Good luck with your application process!