You'll want A or B.
Creative S/W Synth is some Ensoniq acquisition cruft. That doesn't use soundfonts, you won't want that.

Set the MIDI device to use A and have Duke3d use General MIDI for music while in Windows.

Note that you're not totally finished with setting up Duke3d. You'll want to grab a certain patch relating to the buggy Apogee Sound System to disable the crashy echo code that doesn't like PCI sound cards.

Thanks for responding.

Will try to use A and B and get back to you. I think A was the first one selected by default but will try again.

Is there a really bad soundfont to try to hear the difference for testing. Lol

I already had the game crash without that pci soundpatch. Thanks

I have duke,shadow warrior and blood tweaked with the pci soundpatch, bmouse, and lfblim.

Since you have active SB16 emulation and Creative S/W Synth (and not MS GM/GS Soft synth) it's more than likely that you have VXD drivers installed. I think leileilol pointed out in an earlier topic what your problem can be.
Under Win98(SE) you can use either the VXD or the WDM drivers. The Vxd drivers can only use the Ensoniq based soft synth under Win9x's DOS sessions. But with WDM drivers SB HW Midi synth/SF2 soundfonts should work in DOS sessions. So with VXD drivers only Windows programs/games can use the HW Midi synth of your SB Live.

@ leileilol

Just getting back post about my results.

I tried all 4 of those Midi selections and nothing changed.

@ Falcosoft

Indeed I have the VXD drivers installed. Tonight I did install the WDM drivers as well as the dos drivers. Loaded up soundfont that crashed my computer while loading (must be those WDM drivers as this wasn't a thing with VXD's). I Went through the midi selections again and when I got to the MS GM Synth I noticed the music got louder than before but not better.

Anyways trying to change out soundfonts kept crashing with the WDM's. I just did a reinstall of windows (only about a 2 week old install anyways) and got to try out my Unattended install file which worked rather well. I did install the VXD drivers again. In the end I think soundfonts are for true ISA cards or DosBox on XP/7.....

Want to say thanks for the help though.

One option you got is using VDMSound for MPU-401 emulation with the VxD drivers.