Mike, just a friendly tip... if you have not already you should check out the new clip grouping in folders options in X3. It's been a while since I looked at it and I am doing other stuff so I won't type up a step by step but if the problem is what I'm thinking it is then all you have to do make sure you have "Group Clips in Folders" (or whatever it's called) selected in your recording options, set up track folders for each multi mic set up (like if you have three mics on a guitar put them in a folder or full drum kit setup put them in a folder) before pressing record and all the clips being recorded into that folder will be grouped on a take by take basis (meaning if you stop recording the clips generated from the three inputs from your guitar will all be grouped for editing because they are in their own track folder and all the individual drum clips will be grouped because all those tracks are in their own folder, etc). Start record again and a new clip group will be created in each folder for each track so that way all the takes from the first pass can be edited simultaneously without affecting the second pass and vice versa.
I'm pretty sure (but am merely speculating) that this feature was introduced in X3 to solve the multitracking dilemmas people were facing after the 8.5 to X series changes. I've worked through many live scenarios in my mind trying to find a situation where layers would be superior to the folders grouping option in this regard and simply cannot visualize one. I do not however work in any multi musician live room scenarios anymore but it has solved my scaled down multi input issues (multi in recordings in my home setup) and adding extra musicians and folders does not seem like it would cause a problem.
Just right click the Record button in the Transport Module and the Record Preferences will pop up. You will see the options for this in a dropdown menu a little ways downscreen. It has helped me immensely.