Unfortunately, those boxes you checked do not do anything with your GEDCOM entries. Their only purpose is to indicate that we are done with a particular record (either it's been added to WikiTree or we decided to ignore it). You are not alone -- many members have mistakenly assumed that the checkboxes had a more significant function.
The good news is that you have finished processing your suggested matches, so you now have "ADD" buttons for the records in your GEDCOMpare, and you can start ADDing profiles. 
I think the "ADD" process works best if you start with a record for somebody who has been "Matched" to an existing WikiTree profile (maybe your own profile), and click the "compare" button at the righthand side of the row. That should open a COMPARE screen where you can see that person's family group as it is configured in both your GEDCOM and WikiTree. Use the "ADD" buttons on the left side of the screen to add your GEDCOM data to WikiTree, one profile at a time. For best results, I suggest that you add a person's parents before you add their siblings, and add spouses before you add the children. When you've finished with one screen, choose someone else who is "matched" (maybe one of the people you just added) and open a COMPARE screen for them.
