not sure what the main issue is with the tone? too harsh? compressed? treble? bass? muddy? but here's a few things to check out or consider.
when you're dealing with hotter (higher output) pickups, things are a quite a bit more sensitive all around. if you don't already, try setting your guitars volume at about 7 or 8. this will buffer the output of the pickups and allow the pedal tweaking to be much more forgiving.
a lot of beginners (not saying you're a beginner, just in general) ignore the guitars volume knob as a tone control option. they just crank it to ten and chug. the volume knob on your strat is designed to roll off treble as you decrease it... giving you a smoother sound through the 7-10 range then from 1-5 it strats cutting volume significantly.
as for the amp, not sure what kind of marshall you have but they have a harsh tone to begin with. that's their brit showing. try to clean up the amp by dialing back the bass... remember you're playing through a boss effects pedal as well. it's a digital pedal that's going to put out a compressed signal... i've always been partial to analog signal paths for that reason but i understand completely about the simplicity... i have a podxt live that i used for quite awhile live for that same reason.
anyway, these are some things that might make your tone a little more manageable. remember that volume knobs are critical in live applications.