First things first, thank you Vera for selecting my answer as the best.
If you mean those folks you click on the completed box because you don't want to add them Vera, I do see your point. This may change in a future revision of GEDCOMpare, but at this time, we have to do what the program wants. As I said, changes are made from time to time to facilitate users wishes.
As to viewing your FTM and GEDCOMpare at the same time, this is based on your computer's operating system and your browser's capabilities. This is outside of the WikiTree purview.. Not much WikiTree can do there. I am not good on MAC computers and their functionality, but you can use a split screen in Windows to have both open at the same time side by side. The down side is if you have a smaller monitor, the size of each window can make reading them a bit difficult as well as making you have to scroll not only in the vertical, which is normal, but also horizontally, which can be a real pain in the neck.
Newer Windows based computers permit you to add a second monitor to your computer so that you can have WikiTree on one screen and FTM on the other and use some protocols to allow you to work on both of them. Much easier on the eyes. You would need to check your computer to see if it supports this function.
GEDCOMpare does the search for duplicates for a group of names. When you manually add a Profile, the search for existing Profiles seen on the Add page is the same for just that name alone. Be aware that when you do get to add names after completing all of the Suggested Matches work, when you Add the name you may still see additional possible Matches on that page. Why? GEDCOMpare only shows 5 Suggested Matches on the Report List Page per name at a time. If you have a common name you are adding, say John Smith, there may have been more than the screen could show. The Add page will now show those additional possible Matches.
OH, one other thing, Some folks complain that hey, I matched my name to an existing Profile I created, why do I still have to Match or Reject the other Suggested Matches for that name? Because the possibility is still there that yours is not the only Profile on WIkiTree.
As Chief Dan George said in the movie "The Outlaw Josie Wales", you "must endeavor to persevere". OK, not a great ending quote, but you get my meaning. :)
Good luck and any more questions, G2G is always here.