I use two GT-3's with a pair of Peavey Classic 50's. Boss suggests you route the GT output to the amp's clean (normal) input for combo amps. Check your utility settings to be sure your GT is set for combo, and not headphones or line out. This allows you to adjust EQ, presence, etc. on the preamp section of your Marshall. If you're running preamp simulators on the GT-6, set the Marshall very clean.
I have had some luck plugging the GT output directly in to the effects return (or power amp in) on combo amps. Change your GT settings to Power Amp if you do. None of the knobs on your Marshall will have any effect, you're running everything from the GT. This is a little more tricky to control.
You can also use a "four wire" method. Check out Boss GT Central to look it up:
http://www.bossgtcentral.com/index.phpI use this hookup because I love the sound of my Peavey's preamps. But, it is rather complicated (hence the link), tricky to balance and it is more difficult to keep noise out. Basically, it lets you use the preamp section of your Marshall as an External Overdrive. Might want to get a better feel for the GT first.
Couple of tips to get a little more bang from your GT.
Back off the Master Level (volume) settings for your patches and pump the levels of the primary effects. For example, if you are running a Preamp simulator full time on a patch, pump the level up on it to 60%+, back the patch master level down to 30%. Toss in an EQ and set it's level way up. You'll hear it.........
This only works for effects that are on full-time on a patch. Efffects that you may turn off and on should not change your level too much (like delay, compress, chorus)
You can put any patch in "manual" mode which allows you to turn on/off individual effects within a patch. This has no gap - the effect turns on instantly. In manual-each footswitch controls a seperate effect. These are assignable too. You can even assign the Control pedal to toggle from normal to manual mode. Very slick.
Learn to use the Pedal assigns. This will open a whole new world to you. You can assign the control pedal and/or the expression pedal to do multiple things at one time (thru the assign 1, 2, 3), For example, when you hit your control pedal- turns reverb level up 5%, overdrive pre-gain up 25%, preamp sim level up 5%= instant lead guitar! Assigns like this to the expression pedal can give you some big swells, feedback helpers, fade outs, etc.. The list is endless. Get good at setting these up and think about adding another (sub)-expression pedal like a Roland EV-5.
Play with the GT's unit main output level control. Try 50%, 70%, 30% etc.... Amps respond differently to the input level.
I once thought a "Sweeping Arpeggio" was an Italian janitor.