You can certainly do that. A few things to consider:
- The AxeFX has its own effects loop, and you can put it anywhere in the signal chain that you want to. It can be different in each patch.
- The AxeFX has really great effects. My pedalboard was full of boutique pedals... Strymon, Keeley, Empress, Xotic, etc. Once Fractal updated their rotary pedal in FW 18, I sold the last of my pedals. I'm very picky about my tone, and the AxeFX is really this good. Given the arsenal of effects, and flexible signal routing, you may find you don't need all (or perhaps any) of your current pedals. I even use a wah pedal model that is controlled by a Mission EP-1, which looks / feels like a CryBaby wah, but is an assignable controller.
- The Amp / Cabinet models in the AxeFX are incredible. This is where the unit really shines. Most of my patches have two amp heads, each routed to a dedicated cabinet, each with its own effects, then internally mixed to a stereo output. The Boogie Lonestar model is absolutely perfect - to the point that I sold my actual Boogie Lonestar! Same for the other boutique amp models. Definitely consider using the amp / cabinet / microphone modeling as well.
I've played for a long time, and since I got the AxeFX, I've been told by many FOH sound engineers "that is the best guitar tone I've ever had at the board." I don't work for Fractal, and I don't get anything for recommending their equipment. I'm just a really satisfied customer.