Have you tried setting levels with NO Native blocks in the signal path? Set your input levels so you get a nice clean DI level. Make sure you don't overdrive the Native input setting (use -12dB for starters). You should have no problems getting a good output level into your DAW track unless there is something wrong in your hardware (bass, DI, Scarlett, or cables). After you get a good level, add an amp block only (with no cabinet). Start with the default settings and adjust. All still good? Then add a cabinet. Add blocks as needed, checking levels along the way.
Troubleshooting: start simple, then add stuff. Let us know how it goes.