I use the clean channel about 20% of the time, ch.3, 30% & ch.2, 50%. I have my clean dirtied up so that when the guitar volume is all the way, it gets kind of meaty to where ch.2 picks up from there at half volume on the guitar. Ch.2 has the gain at 9-10 o'clock pushed in. Ch.3 has the gain at 3 o'clock pulled and can sound similar to ch.2 when at half volume on the guitar. GEQ2 is set for a lead boost for all channels.
"Mark Knoffler to Pantera on one amp, impressive" as quoted from last Wednesdays open mic.
That's exactly how I use mine. Set each channel as dirty as I'll ever need it and use the guitar's controls to bridge the gap. The clean channel has beautiful breakup with all the EQs cranked and can still get sparkly bouncy clean when rolled off. Absolutely seamless. I used my V the same way but if anything the JP sounds even better for my needs. From Beatles to SRV to Thin Lizzy to VH to Metallica to smooth Petrucci leads all from the guitar's controls. Heaven.