Need Help using Axe III through EFX Loop of Mesa TC-100 (the problem is with the Axe III, not the amp)

If you want to for example put wah, drives etc in front of the amp before the preamp and then your modulation effects like chorus, delay etc after the preamp so in your FX Loop you'll need to use the 4 cable method that would be p27 of the manual. P29 refers to just putting the axe in the front end of your amp not the FX loop.

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in the online manual P29 is for post, P30 is for pre.
 
Any other suggestions on why the tone is changing so much when I instantiate effects blocks?

Keep in mind that when you’re playing through the front end of you’re amp you’re utilizing the preamp controls. When you switch over to effects loop you’ve now bypassed the preamp and the tone controls no longer have an affect. This is why you hear such a drastic EQ difference. Either play through the front end or back end because switching between the two will require completely different tone settings in your Axe presets. You can do it but you’ll have to create different presets or scenes for for using the preamp in your amp or not.
 
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