Due to the instrumentation in alot of the songs we play (Our God (Jeremy Camp), Jesus Saves, Where The Streets Have No Name, Spirit In The Sky etc..) I like to have an acoustic but have the ability to add some overdrive on the choruses or at other times in songs.  So here is my setup.

Godin LGX with separate acoustic and electric 1/4" outs.

Fender American Deluxe Ash Strat with LR Baggs X Bridge and LR Baggs pre amp built into the guitar.  (I have been using the Godin for years, but just had the Strat setup with the LR Baggs system.  The Strat will have a TRS cable stereo signal, but will work the same as the Godin.)

Pod HD 500

Two Phil Jones Cub 100W amps

I have two guitar cables that I use cable ties to keep together.  I have them joined about every 5 feet with enough of a split at the end to separate the Cubs 6 feet apart. 

Electric output from the Godin runs to the "guitar" input on the Pod HD.  Acoustic output from the Godin runs to the "Aux" input of the Pod.

XLR outs from the POD run to the PA Board so the house controls the mix.  One is acoustic, the other is electric.  Each 1/4" out from the POD HD500 runs to the Phil Jones Cubs on stage.  I get a separate electric and acoustic signal path to each of the Cub amps as well.  The Phil Jones Cubs work well for both types of signals as they do not color the sound and come very close to working like PA speakers reproducing the sound accurately and they weigh about 10 pounds each.  It works better if you spread them out as far apart as possible facing the congregation, but about 6 to 8 feet works well.  If you use them for monitors facing you then they can be right together. 

There is a tone available on this forum that I just pasted into 4 separate "user tone" sections on my Set List of the POD using HD Edit.  I then setup the signal paths for Electric and Acoustic.  There are some great acoustic sounds available on the Tone site.  On the Electric path I setup the volume pedal so I could fade the electric in when I need it.  Works great on songs with building dynamics and on choruses.  The dual tones of Acoustic and Electric complement each other well if you want to use them all the time.  I use the acoustic and a nice clean Blackface setting together often.

I have one of the footswitches on the POD set to add an overdrive pedal, so I essentially have a clean channel, overdrive channel and four different electric amp sounds with a jumbo acoustic on three of the channels and a 12 string acoustic with the other with the ability to take the acoustic or electric all the way out at any time.  All this on four POD channels, so no changing banks in the HD to find sounds while playing live.