Last night after the band played and the club cleared out I went and setup the 4 cable method to give it a try. I didn't want to actually do the gig with 4CM until I was familiar with it, so I haven't tried it with the band yet but I heard how it generally sounded.
I noticed when I ran the time based effects (reverb, delay) into the fx loop they sounded more clear and pure which was good. It still seemed like the distortions were the same, when I go to the low register of the guitar I get this ridiculous 'farty', rumbling, non dynamic sound. The distortions do sound decent in the mid range of the guitar neck, but its important to point out that everything sounds alright when I'm playing alone but with the full band its a totally different story.
Rd2rk said I should run the distortions before the effects loop, sending them straight to the marshals preamp, as far as I understand this is what I had been doing before and it won't change my main problem, that being the sound of the harsh and 'boxy' sounding Helix distortion blocks.
What I've been doing with the band for the past few nights is setting up my Helix with 2 cables and using a 3rd cable to run my Ibanez Tube Screamer stomp box in front of the Helix. I just use the Helix for reverbs, delays, modulation effects and wah, when I need distortions to play a solo I kick on the Tube Sceamer stomp box and everything feels and sounds normal again and I can play happily. So I'm attributing my problem to the nature of the Helix distortions.
Maybe it's just the way the Helix sounds through the front of a guitar amp (again this is a cheap lollipop marshal combo) and it would be great through a PA or flat response speaker. But It seems really weird to me that this is such an expensive and prestigious piece of gear and when I'm presented with a totally normal scenario, a stage with a guitar amp, it's basically 90% unusable to me. The ship is in Europe right now and I'm going to give it another month of experimenting, but I might try to find a music store somewhere in Spain or France to buy my Helix used and I'll then buy or order an analog pedal setup because I'm going to be on this ship for most of this winter into the spring and I want to have a really reliable setup so I can focus the majority of my attention on musical things.
I'm still really interested in hearing some insights so if anyone can tell me what they think, or if I'm clearly not understanding something please let me know. Again I am pretty much a gear noob because I've just been an vintage archtop obsessed jazz player for most of my life.