My layout is connected similar to what wmwalker posted above. I don't have any issues either they both work great together.
The MTH engines will only operate as either conventional or with the DCS Remote controller. I operate my Lionel TMCC engines with either the Cab 1, Cab 2, or the DCS Controller. The majority of the time I use the DCS Controller because of its flexibility. I have two Lionel Legacy engines, again the majority of the time I use the DCS Controller for them as well. About the only time I use the Cab 2 Legacy controller is when I need a 3rd controller for someone to use. Or to "show off" the Legacy features. In my opinion those features are rather minimial. (Vibrating hand set, Quillable whistles on a few engines, Braking feature.)
The other BIG advantage is I have ALL my switches AND accessories connect to two AIU units. Thus with the DCS controller I can control all my engines, switches, and accessories with the one controller.
The advantage of having both systems is significant! I can purchase ANY engine I desire (assuming $ is not a concern) The systems coexist fantastically.
As you mentioned a line dedicated for Conventional. I too have some conventional engines I wanted to be able to run. A HUGE advantage of the DCS system is that you can define two lines as "Variable" lines meaning you can vary the voltage on that line WITH the DCS remote. Makes the conventional trains operate as IF they were command control. Of course you can only have one engine at a time on that line.
As you discussed whether you should get both systems or not? I have all 3, TMCC, DCS, & Legacy. If you plan on being around in the hobby for awhile, and see a possibility of adding to your roster, or interested in a lot of the new features that are and becoming available, there is no decision. I strongly recommend having both systems! Even if it means not getting an engine that you want in order to get the system. It will pay off in the future.
You also asked about running the systems together. I routinely run on the SAME track DCS, Legacy, and TMCC engines at the same time. No problems! . (It gets a little tricky to try and also do the conventional engine, due to the higher voltage on the track 14-16v,)
Hope this helps, HAVE FUN!!!