There are a whole bunch of ways to do this... I went through a hell of a process figuring out exactly the way I feel is "right" with my equipment for the types of projects I'm working on.
The very first thing I did, was work with my guitar itself. I did this with
my Boss GT-10 pedal because I wanted this part for live performances as well, but the process drastically improved the quality of my guitar. I plugged the guitar into my pedal and listened clean. Then I took note of what I liked and didn't with that clean signal, and EQ'ed it to my liking (at this point, mostly just removing "bad" qualities). Then I added my Marshall amp and dialed that in to something close to what I like, without the use of the EQ above. Then I A/B'ed the EQ to see if that was actually helping or not, post amplifier. Then I added another equalizer after the amplification to address other "bad" qualities that arose from that. Then I moved my equalizers around so both were before or both were after the amp, both on either side of the amp, and then with both of them off. I really tried to figure out how to make my guitar sound as good as I could with my live rig before I went anywhere near the recording equipment. This process took days before I finally settled on some stuff.
After I dialed in my base "sound", I went on to just play with every other effect I use or thought I might want to use, and I put them all over the effects chain to figure out what each thing was capable of in various areas of the chain. The biggest difference seems to come from pre/post amplifier effects, in my experience. For a quick example, hook up a wah pedal before your amp, and then in your send/return loop (so it happens after the preamp does its magic)...the wah behaves quite differently.
Just as an example, my effects chain looks something like this...
Guitar -> EQ -> Compressor -> Wah -> Amp -> Gate (just to kill amp hiss after amplification) -> EQ -> Chorus -> Flanger -> Volume Pedal -> Delay -> Reverb
Only after doing all of that, did I start recording. Once I got that all squared away, I decided that it was best for me to record my guitar completely clean, straight into the computer. This way, I could focus on the performance, I could hear any mistakes easily, and I can take that clean signal and plug it into my guitar rig to record the actual "guitar sound" I want. It may seem like extra work, but in the long run it can save a good deal of time if the performance is perfect, but you want to just change a few settings with your amp or your effects. If you record with the effects applied already, you're stuck with them. Not necessarily a bad thing, but not all that great if you're unsure of your guitar sound.
There are some general guidelines and standards, but no "right" answer (as you'll hear a lot around here). Look up anything about guitar effects chains and you'll get several schools of thought...all interesting, but not all applicable to all situations either. You could also try asking in the guitar forum about effects ordering, I'd bet.
Hope that helps!
And yeah...editing the clean guitar "performance" lets you really hear if your edit job is smooth or not. For me, it goes right along with finding bad notes and what not. If you get it sounding good completely raw, you're on a fantastic start to a good guitar track. Definitely a good call here too.
