Thats a toughy before even getting to the additional questions!
i dont use Reason & I've never used the motif 6 so dont know its ins and outs.
try these.
http://www.motifator.com/forums/showflat.php?Cat=1,2,4&Board=MotifClassic&Number=394979&page=&view=&sb=&o=
http://www.yamaha-motif.net/
Getting midi from the motif into cubase is simply a case of hooking up the motifs "midi out" to your pc "midi in," and if the motif has a "midi in" connector, you could connect that to one of your pc midi interfaces "midi out," that way you can sequence/record midi in cubase and have your motif play the sounds you want, then record the audio into an audio track in cubase, this will require an audio interface or you could simply plug your motif into your aux in on the onboard soundcard, although chances are that this will not sound as good, and either way you do it you will almost certainly have some latency between the midi playing and the audio from the motif being recorded/played in cubase.
Unless you sample all your motifs sounds into cubase (i've done this with just the notes/samples i required from an external synth) and use a sampler like kontakt, there is no way to get your motif sounds playing from within cubase to a midi track. Check online; someone may have already gone to the trouble of putting all the motifs sounds into a soundpack for one of the many ROMplers & samplers compatible with cubase.
As for your other midi devices, if you cant route them within cubases preferences and midi channels, might I recommend MIDIOX, a free program that i use in my DJ setup that makes virtual midi ports so in theory you could just use it to route your keyboards to your external modules, although I couldnt even begin to suggest how you could add cubase or reason to that mix!!
Try cubase's preferences first, you should be able to use all your midi ins and outs, then select those individual midi channels ins and outs once you've created/selected them, over on the left of the project window under "input" & "output."
Seems you have quite a cool setup, just an issue of routing which in cubase is relatively accomodating & easy to set up.