If your set is balanced (and yours is), you only need to adjust the truss rod tension.
I play downtuned drop C# with flats, and agree with father of fires. It depends on what you like. Yes, it will sound "muddier" than rounds, very dark, but that's why you have an amp and that's why your amp has EQ. Don't be afraid to cut the lowest frequencies on your bass or on your amp and boost the mids, it will sound magnificent (IMO). Also depends on the style of music. If you play funk, that might not be the best option. I play mostly rock and blues, and it gives me great tone.
Notice, though, I play my low C# on a .110 gauge. At first it felt very hard on my fingers, but it's a little less sloppy tonewise.