Note that this Gedcompare is a brand-new feature, so none of us has much experience with it yet. And I can't see your Gedcom,
In Gedcompare, if you COMPARE Jane Blackstock, you should see a screen with two columns that list Jane and her family group. The left column is Jane in your Gedcom, with parents, siblings, spouse, and children. The right column is Jane on WikiTree, with the relations that are mapped for her in WikiTree. You can't see Jane's whole family tree in that screen (I've also found that it's helpful to refer back to my other family tree when I'm using Gedcompare), but it suffices for the purpose of ensuring that I'm editing the right people. If there are people on that screen who are in your Gedcom and not on WikiTree, you should see an ADD button that invites you to add their profiles. I like to work to work from the Compare screen. My experience indicates that the family relationships in your Gedcom will be preserved if you add the profile of one of Jane's parents, her spouse, or one of her children. You can also add her siblings from that screen, but don't do that until at least one of her parents is in WikiTree. (And check the completed profile before you go on to the next one, to make sure everything looks right and the family members are getting connected.) You really can build out a tree pretty quickly by adding one person at a time, with connections to their immediate family members.
As for those maternal ancestors, probably the best way to add them will be to start with your grandparents who are already in the tree and add the previous generations who are in your Gedcom. As with Jane, start in a Compare screen that includes people in WikiTree, and work from there.