you have a sequencer with two midi ins and outs. One keyboard in,out,thru and two modules in,out,and thru. Follow me so far??
the midi keys are connected to the in and out of the sequencer. One module is connected to the out of the sequencer via its midi in. Now, the other is connected to the thru of the keyboard via its midi in. The
question is how can you control the second module without messing with the info you've sent to the keyboard already or do you control the second module from the keyboard???

bigskee:
You have three choices here, only one of which (throw money at it) do I have direct experience.
1) sysex messages identifying hardware. Your sequencer would have to be capable of sending system exclusive messages causing specific hardware to ignore certain MIDI information. I'm fairly certain this is possible, but I've never done it, and I have no idea how.
2) setting specific hardware to only receive specific channels. This is, I think, somewhat easier to do, but requires that your keyboard and in-line modules be able to shut off playing the contents of specific MIDI channels. I've actually read the documentation on how to do this, but, again, I've never done it.
3) Throw money at it. MIDI patch panels take care of a host of multiple-MIDI-device problems. They can be configured to distribute certain channels to certain MIDI-out connection points, which eliminates the need to configure your modules. If your sequencer is your computer, you can designate which patch point gets which MIDI line from within your software. In addition, since a MIDI patch panel is a reflector, it eliminates any latency inherent in daisy-chained setups.

My MOTU MicroExpress was, if I remember, under $200, and was one of my first MIDI purchases. It has made expansion of my module capabilities way easy!

I'm not your best source of information, but I hope this helps some.

Midi Patchbay