Tone/gain controls are all usable on the same settings. You pretty much want them all straight up on chan 1. Using all three modes on one song? That's a bit more difficult, but achievable. The problem is the volume differences. Some people use the 2 different master volumes and switch them. You can also get something like a G system and set the patches for volume compensation. The best suggestion is what Peter suggests. Use it like it was intended to be used. A 2 Channel amp. You can change modes between songs. I have no problems using it this way. Channel 1 mode 2 "Texas" cleans up really nicely with a volume roll back or a light pick attack (i use that more than vol pot). It can also get as or more gainy than JCM 800. I use it 75% of the time. When I go to lead I either switch to channel 2 or use the 2nd master volume as a boost. Channel 2 provides a good distortion sound. I still mainly use it for solos, but when I need it for rhythm its good. Channel 1 mode 3 is a nice pretty tight distortion. I use it for heavier songs that don't clean up.
so short answer: You can make it work for you somehow. It just takes some playing with to get it working nicely. I recommend you play with it for awhile to figure out how you'd like it to operate and then consider the mode changes.
If you absolutely HAVE to have more channels with different EQ's etc get a VH4 or Herbert.