The first step in working with GEDCOMpare is to review the suggested matches. After you have accepted or rejected every suggested match in the file before you will be able to see ADD buttons on the main screen in GEDCOMpare. (Before then, you will occasionally see ADD buttons for some people -- when you open up a COMPARE screen that shows a family group in which there are no suggested matches remaining to be processed.)
Once you have finished reviewing suggested matches, I recommend (based on my experience with the new Gedcompare) that you open a COMPARE screen for someone in your Gedcompare who is metched to a profile in Wikitree (maybe this will be your own profile). Use the ADD buttons displayed on that COMPARE page to add profiles for that person's immediate family members who are already in WikiTree. If you always work from people who are in WikiTree, and add their family members, you should preserve the connections between family members. (On the other hand, if you ADD isolated profiles from the main screen, you are likely to lose the connection information from your GEDCOM.)