No, that little checkbox on the left on the GEDCOMpare report doesn't do anything whatsoever to WikiTree. All it does is mark that person as no longer of interest to you on the report, that is, if you tell it to "hide completed rows", it'll stop showing everyone with a checkmark.
Step one after running a GEDCOMpare report is to accept or reject all of the possible matches that it suggests. These are in the right-hand column of the report.
Once you've dealt with every single suggestion, the right-hand column will have an "add" button for each person. If you don't see "add" buttons, you still have a pending match.
The "add" button takes you to the same "add person" screen as you'd get using any of the "[relationship?]" or "[add child]"-type links in WikiTree, except instead of a blank form, you see your GEDCOM data transferred to WikiTree's fields. If your file contained unusual information, chances are the transfer will not go smoothly, and it is my experience that the process mangles sources, sometimes beyond recognition, but I do like the fact that I don't have to retype the dates and places and such. (This greatly reduces the chances of new typos.)
When adding people from a GEDCOMpare report, it is best to start with immediate relatives of someone who already has a WikiTree profile. This way, the relationships are automatically transferred.
