Fender Amp Tips
Fender amps have a LOT of bass. The exception, as Jay noted, is the Bassman, which is what a Marshall is actually based on. If you do a neutral boost into a Fender model you're going to get a flubby, loose, bottom (that doesn't sound quite right, but you know what I mean ) I would recommend using a drive model like the TS808 or similar model that has a strong bass roll-off. I'd also lower the DRIVE in the amp block. Most people run Fenders with the volume around 3-4. A value of 8 is going to be muddy since as you turn the drive up the "Bright cap" is being taken out of the circuit. Fender's were designed to reach full rated power with the volume (DRIVE on the Axe-Fx amp models) at around "4".
The general idea when going for a distorted tone while using a Fender amp is to let the pedal do the distortion ("clean amp with pedals" paradigm). If you drive the amp the bass is going to get flubby.
To get a clean sound - set the midrange, where present, to ~8 and bass and treble very low (1-3). This requires running the volume at a higher setting than 3-4 to get maximum power. It also defeats the operation of the bright cap, if it is not switchable. That is my intent. If it is switchable, then I turn the "Bright" switch off.