Like this...
JK It depends what i'm trying to do. Usually I think about where the signal is going after my Axe FX. For instance will it be going through a PA, running through a power amp and real cabs, into a DAW etc... Then I think of what kind of a sound i'm looking for. Imagine what possible effects I might want, do I want something unique like a synth or is this going to be a high gain tone.
Once I figure out what I'm looking to get and where the signal will e going after axe fx I try to imagine signal flows in the axe fx grid I think will get me there, think about any parallel routing I might want to do etc. Then I try to look for an amp and cab(unless i'm running into a real cab sometimes I will omit cab block or ad it later for a unique sound). Then I think of any blocks I will be running pre amp like compression etc... Then I get settings on amp and cab reasonably close to the gain staging I think I will be using when I'm finished. This is so I can dial in the input noise gate. I am more aggressive with Input gate if I am making a High gain patch.
Then I add drives, compressors, or anything else I want before the amp. From there it all really depends on what I'm looking for. I consider the character of the reverb I might want to decide if I want parralel reverb from the input signal, from after an amp or cab or serial pre/post amp/cab. It all really depends.
If I was on the spot desperate to dial in a tone really quick I would say your system would work pretty well for getting a good usable tone I would be satisfied with immediately and down the road.
For me there are so many possibilities I can spend hours experimenting with different signal flows and settings to get very unique tones not really attainable with anything other than axe fx.
My best advice is once you are familiar with the amps, cab and effects blocks, unless you just want to fool around for a long time and make really cool tones, would be to start with an Idea of what you want to sound like. After enough experience you will get a feel for what different amp models, signal flows etc... will get you in that vicinity. From there take into account the tonal characteristics of your guitar, poweramp(if you are running through one), etc. Think do you want a straight up mono signal chain that might sound like a standard guitar amp with pedals running serial into it or huge sounding guitar that running two amps and cabs stereo will get you? Do you want your reverb to be clean(straight from guitar input running parralel) or distorted(running serial before or after amp).
There is really no right or wrong way to do things. That's the best and worst part about axe fx. The possibilities are limitless but sometimes if you don't add certain constraints to shaping your tone you may look up at the clock and see hours have gone by while you have been dialing in the perfect tone you want. There is so much you can do it can feel overwhelming at first. If you have the time I would advise playing around with alot of different signal paths and ideas and parameters(isolated as much as you can) and try to get a feel for how different settings work and interact with each other.
Good luck on your quest for the ultimate tone
It certainly is weird getting used to the creative power of axe fx. Before that for me it was as simple as running through a gate, overdrive pedal, maybe a few others turning a few knobs on a tube and and that was that.... With axe fx it can be that simple and sound amazing but you can get so deep into tone shaping it is mind boggling.