If I don't recognise a match but can build their tree backwards I'll create a floating branch based on that match. I add the shared cM in the suffix box for easy reference in tree view and give them a custom profile picture so they stand out. I also link them to the tree from the dna match list page.
I work back down their pedigree line generation by generation and push each generation as wide as I can. If I find 10 children in a generation then I'll add them and try to add the spouse(s) for them too and when possible bring those branches forwards to the present day as best as I can.
I'll then go to the shared matches and find the closest relative to my match using protools, I then build the tree of that closest relative they have and do the suffix/linking/profile picture as above, the goal is to get to the point where the two trees merge, in many cases they attach to one of those wide branches I've already built. I repeat the process for as many of the shared matches as I can aiming to have a tree showing how they all link to each other. Final step is to add a custom profile picture to the ancestors of each match, this is done so that in tree view I can easily see branches that have dna descendants and those that don't.
Yes it's a lot of work and I won't pretend it is always easy to do but I've had new matches that pop up who are already in my tree or maybe their parent is, I've already done the hard part building the tree so it's quick and easy to do the linking/suffix/profile picture. I've managed to link as many as 40 matches to each other, identify the common ancestors and identify if it's a link via their maternal or paternal side, that saves a lot of wasted effort researching the 'wrong' parent which is a bonus too. It's independent of Thrulines so avoids the no tree/wrong tree/private tree issues. Another plus is if I create a WATO tree (What are the Odds tree), I already have the cM figures in plain sight as the suffix to the name, there's no need to flick from one site to another and switch between matches for each of them.
It's hard to explain and I can imagine it's hard to follow when reading so I'll add a screengrab to try and illustrate it in next reply