There is a way of doing it but it is very time consuming.
What you need to do is unpack TWG someplace other then the sh3 install location, then go into the data/sea folder (also data/air if you want to do the same for aircraft). Each folder in the sea folder is a ship or sea object. What you need to do is copy the ****_shp.tga file for each ship from the TGW to your install folder, replacing the exisiting ones (you may want to backup the install folder first). You dont need to copy over the ones for ships that dont exist in stock.
Next you will need to go to data\Menu\Gui\Units in TGW and copy all of it over, and lastly you will need to open maps.cfg (in data\Menu\cfg) and compare the 2 of them in notepad. What you are looking for is this...
Code:
;units military symbols
;MatSymbXY where X digit means the type of the unit/convoy and Y digit is the size of the convoy (0 for small, 1 for medium and 2 for large)
MatSymb00=0x3B,0x0B,data/menu/gui/Units/UnitWShip.tga
MatSymb01=0x3B,0x0B,data/menu/gui/Units/UnitWShip.tga
MatSymb02=0x3B,0x0B,data/menu/gui/Units/UnitWShipM.tga
MatSymb03=0x3B,0x0B,data/menu/gui/Units/UnitWShipL.tga
MatSymb10=0x3B,0x0B,data/menu/gui/Units/UnitMShip.tga
MatSymb11=0x3B,0x0B,data/menu/gui/Units/UnitMShip.tga
MatSymb12=0x3B,0x0B,data/menu/gui/Units/UnitMShipM.tga
MatSymb13=0x3B,0x0B,data/menu/gui/Units/UnitMShipL.tga
MatSymb20=0x3B,0x0B,data/menu/gui/Units/UnitSub.tga
MatSymb21=0x3B,0x0B,data/menu/gui/Units/UnitSub.tga
MatSymb22=0x3B,0x0B,data/menu/gui/Units/UnitSubM.tga
MatSymb23=0x3B,0x0B,data/menu/gui/Units/UnitSubL.tga
MatSymb30=0x3B,0x0B,data/menu/gui/Units/UnitAir.tga
MatSymb31=0x3B,0x0B,data/menu/gui/Units/UnitAir.tga
MatSymb32=0x3B,0x0B,data/menu/gui/Units/UnitAirM.tga
MatSymb33=0x3B,0x0B,data/menu/gui/Units/UnitAirL.tga
MatSymb40=0x3B,0x0B,data/menu/gui/Units/UnitLand.tga
MatSymb41=0x3B,0x0B,data/menu/gui/Units/UnitLand.tga
MatSymb42=0x3B,0x0B,data/menu/gui/Units/UnitLandM.tga
MatSymb43=0x3B,0x0B,data/menu/gui/Units/UnitLandL.tga
Make sure that part of maps.cfg is the same for both, if it isnt then change your stock version so it is.
I think thats everything
SH3 commander i cant answer your question on as i personaly dont use it. But i think the files are contained someplace in its install folder, try digging around with notepad