Off the bat, I 'read' the channels on the mixer from left to right I dislike the way Reason adds new channels to the right - plus there aren't enough colours available.
Anyhoo, that said, I usually end up spending time at the end of each session sorting out the sequencer lanes and mixer channels into 'zones' and colours, and arranging the rack accordingly, a column per division.
The mixer and sequencer follow the same routine, seq from top to bottom and mixer from left tonight, labels are of my own making and may not mean the same thing to anyone else;
Reference track (wheat)
Bass (dark blue)
Sub-bass or alt bass (slate blue)
Lead (kelly green)
Melody (mid green)
Alt LEAD/melody (light green)
Pads (pale blue)
Any automation lanes I like to have red.
I don't like using purple.
The rack is (usually from left to right); vox - drums & perc - bass (and main I/Os) - then the others depend on how many devices with a column for each of the 'zones' on the mixer/seq.
I also, invariably have to start with Redrum using a set from Vengeance, and a instance of Rad piano with the Bill Withers setting, plus one of the Korgs for bass. Unless I'm doing a remix, or reworking a MIDI file, or starting with an idea based on a vocal sample. But within the variety of start up options the format is always the same. Then it all goes to hell.
[I'm rambling, but I'm working on a shite Netbook which is frustrating (PC died last week). Also, I don't have Reason at the moment to check colour names (or even my labelling - haven't run it for a few months now), so all from memory - currently building a new rig.]
Total numpty doin' his own thing for the craic and relaxation - it's cheaper than a therapist, and more satisfying.
'Live fat, die young, and leave a self-basting corpse for the burn up...' - TFC