Hi. I´m afraid I can´t clear up all this for you but here are my way to use BUSses. I´m in Logic X but this goes for Logic 9 as well:
Master: Think of the master bus as the final place in the chain where you can add effects. It does not matter much if you call Logic´s OUTPUT1-2 or Logics MASTER fader your master although I like to think go OUTPUT1-2 as logics master-bus.
Missing effects: If you bounce the whole mix, meaning all tracks, no effects that you hear when you play should be missing when you bounce. Unless you bounce specific buses and solo/mute something. Check your routings again and solo/listen to stuff to make sure it´s really there in the first place. If it still happens, try to route it other ways and see if you can bypass the problem.
BUS vs AUX: Use the send function on individual tracks to send them to buses. Logics mixer will automatically set up an aux track for that BUS you selected to send it to. Hence the AUX IS the BUS. At least in this case.
Just keep in mind the 2 different ways of doing this in Logic, you can send "a copy" of the signal to a bus or you can route the output of a signal to a bus. If you send "a copy" by pressing the send box in the track inspector, remember to turn the little circular meter for how much of the signal you want to send. Holding alt while clicking that circular meter sets the send to 0db send wich might be good. Play around and test. No matter if you use the SEND or route the output of a track to something else than the standard output1-2, logic will make the AUX track in the mixer. The AUX is the SUB buss. They are identical in such a scenario. The AUX will also be named BUS X where X is the bus number you selected from the drop down menu.
Here is a setup of a couple of SUB-groups (buses) and how you could use them.
Your bass sound is made up of 3 bass tracks. Instead of sending them to
output 1-2, change the output to say
BASS SUB MIX (This BASS SUB MIX-bus will automatically be routed into Output1-2 unless you tell it otherwise.) This way you can apply one
plugin for all those 3 tracks on the sub-group.
You can set up several sub groups like that. The advantages are easy to see. Lets say you have some choir arrangements (7 tracks) and a nice pad/strings arrangement (9 track). You adjust the volume perfectly for these 16 tracks by soloing the 7 choir tracks first, later the 9 pad/strings tracks and they play perfectly fine. Later in the mix you find out that you need to carve som space in the 7 choir tracks with EQ, and you need to reduce the volume of the 9 pad/strings tracks and also you need to EQ them a little. That can all be done on the BUS instead of on all tracks one by one. There are a lot of better examples how BUSses can make it easier for you when projects grow more and more complex.
Send your groups to new groups? Yes that is handy if you for exampel want to apply a bandpass or whatever effect to say, just the music/beat but keep the vocals untouched. Then grouping all vocal BUS/tracks to i.e.
VOCAL SUB MASTER and all music SUB- busses to
INSTRUMENT SUB MASTER. These two are again routed to OUTPUT 1-2.
I remember back in the days when I could not grasp the concept of SUB-busses. It is really an easy concept. Just play around with leading tracks to busses.
Really have no idea if this came across as understandable. Feel free to ask.
There is also alot of good youtube videos on subgrouping in logic.