As "desertstriker" noted, GWX 3 Gold and SH3 Commander are separate applications and cannot be installed by JSGME. However, both of them have alternative and/or third-party MODs that are installed by JSGME, so be sure to RTFM...which it sounds like you're doing to begin with.
If you have the hard-drive capacity to do so, I would recommend you put separate installations of JSGME into both the SHIII and SH3 CDR folders; I found it to be more reliable than a single JSGME installation with separate "pointers".
I don't know how much you want to tackle in one fell-swoop, but after several years of toying with different configurations, here's what I've found to be a fairly "comfortable" combination of MODs...(a couple of which I customized with my own added/changed content as well). I confess that I have yet to try the FM_NewInteriors; I spent many years walking around the inside of real submarines and would probably end up nit-picking ("rivet-counting") a lot of things that shouldn't be nit-picked by someone who doesn't have the skills to do such MOD work himself. Anyway...good luck and good hunting!
GWX 3 Wilhemshafen,St Naz,Schluese and xtra ships V6
GWX 3 Xtras Wilhelmshafen campaign v2.4c
GWX_Ships_Buoyance&Draught_mod
GWX - 16km Atmosphere
GWX - Alternative Flotillas
GWX - Enhanced Damage Effects
GWX - No Medals on Crew
GWX - Open Hatch Mod
Aces' Combined SH3.SDL Files v2
Das Boot Officers (plus my changes)
OLC's Modified Searchlight Beams for GWX3
Rapt0r's Das Boot Interior
Rapt0r's Instruments V3.5 [Without Red Circle]
Rapt0r's Uniforms (plus my fixes)
SH-5 Water for SH-3 20 Km V84
Thomsen's Sound Pack 3.2 (plus my gramophone)
TeifeMkI(German)
TheDarkWraith_Ship_Plane_Fire_Damage_v1_4_SH3
TorpedoTubesFireFinal vGW
Xa-Merchant_Fleet_Mod_3.2
Xb-MFM3.2 displacement correction mod
Z-Patch V16B1 (JSGME)