Okay, so I've figured this out. I forgot how much authentic retro gaming made a game out of just getting the damn thing working. I've revised the topic title to reflect the dual soundblaster +SC55 situation to further help anyone who looks up either topics - and also my future self when I inevitably forget 5 years from now
When trying to use the AWE64 Gold for Sound Effects/Digital Card while also using its Gameport for a midi synth like the SC-55 the game will freeze during the intro cutscene. Instead, I'm now using it for just Midi with its Midi I/O set to P300. I have the Gameport disabled on my SBPro2.0 but P330 still seems to have a conflict elsewhere.
System Shock's Install.Exe was throwing an error because while the SBPro2.0 was working in other programs there was a both an I/O and DMA conflict with the AWE64 Gold. CTCM could not run correctly either to initialize the 64gold either seemingly because of this.
Since this machine is a 98SE rebooted into MSDOS 7.1 I had to go into Windows Device Manager to reassign the 64G I/O to A240. Despite the fact that I already had the IRQ to 5 and DMA to 0 (low) and 7 (high) there was still a conflict on DMA1 appearing that preventing the SBPro 2.0 from being recognized. That was simply cleared by initializing the 64G with CTCM which fully pulled over its SET BLAST variables that I configured in the Windows Device Manager: A240 I5 D0 H7 P300 T6. From what I can tell that is all CTCM does, it does not give me the option to set what variables I want the AWE64G to use from within DOS itself. Regardless, that now freed up D1 (DMA) for SBPro2.0 and SS Installer can detect it. I now have SC-55 Midi through the AWE64G MPU and Digital Sound coming through the SBPro 2.0 - yay.
Only having one of these cards would have probably made things go a lot smoother (not sure if the AWE64G should be able to do MPU + Digital sound in SS without freezing during the intro) but I really do like having both Sound Blaster 16 and OPL3 in the same machine with no hanging note issues.
I'm sure now that I've shown that I'm not completely clueless but rather just 'ignorant' more people may chime in here. Feel free to do so! I am very much looking forward to my first ever playthrough of System Shock which I'll be doing blind. Huge fan of Thief & Arkhane Studios Dishonored and especially Prey (2017) so this should be a treat.