help with online applications

When I upload my resume, should I include my cover letter as the first page if there's a spot to paste a cover letter on the application?

I'm starting to apply for jobs and nearly all of the hospitals around here only accept online applications. Typically they require you to create a profile, upload a resume, fill out an application, and submit it for each position applied to. It saves all of your info so you can return later and quickly apply to another job. I have applied for multiple positions at the same facility.

The resume is part of the general profile, and the application has an area to paste a cover letter. I have a general cover letter for each facility, and sometimes there are specific positions, like those in units where I had a clinical rotation that I want to include a more detailed cover letter which indicates I have experience on that floor.

Right now I have my general cover letter as the first page of my resume in my profile, and then I paste the unit-specific cover letter in the application part. I'm not sure this is the best strategy. I want them to read the specific cover letter, but I also don't want the other jobs to get the wrong letter that is specific to another unit. And most of all I don't want them to only look at my resume and think I didn't write a cover letter.

Hope that makes sense. Any advice would be appreciated.