Hi KyleScott,
As you have only one MIDI port connect to PC, the solution withought buying more hardware is defining which MIDI channels will respond for each module.
For example, if you define channel (1,2,3,4) for A-90, (5,6,7,8,9,10,11,12,13,14) for yamaha module and (15,16) for string module, when you select on Cakewalk track 1 channel 1 it will only play on A-90. If you select track 2 channel 5 it will play just on the yamaha module.To make that you have to setup each module and disable the other channels.
To play two modules on the same track on a layering sound, just give the same channel numbers to them.