When you look at the GEDCompare report you'll see all the suggested matches. If any of them are a match, whether they are a profile managed by you or someone else, then yep you should skip them.
The exception is, if you have a lot more information in your GEDCOM for a person (ie sources, parents, etc) then what currently exists in their profile. In those cases, you would mark the person as a match and then uncheck the Skip box. When your GEDCOM is imported those people will be set as Unmerged Matches with the existing profiles and you'd be able to merge the two profiles together at that point. You can only do this up to 10 times in one GEDCOM import though and it's really not recommended unless you do have significantly more information than what already exists.