In a very general sense, putting effects into the front of the amp sends the effects into the preamp- where they are subject to the tone controls and gain. Basically, you take the sound going in to the amp and drive it with gain and EQ. On the other hand, in the effect loop,the signal coming into the effects already has the preamp's gain and tone and then you are adding effects to the "final sound' before it goes to the power amp. That is a very general statement. Also, the input level is different on the signal from the guitar and the signal in the FX loop, and some effects prefer one to the other. So, these two routes can affect how the effect sounds. Some types of effects seem to prefer the clean guitar signal and sound better when gain is added to them (traditionally wahs and choruses or pitch shifts sound better with the front end clean tone, while delays and phase/flanging can sound better in the fx loop). However, there is no right or wrong and what sounds good is subjective.
I am sure there are dozens of folks lining up to shoot this comment oout of the sky, which is fine. The point is the effects "process" differently when they are at the input stage and the loop stage. So, you can experiment and find what suits your ears, style and sound.
Personally, I run my wah, boost and any overdrive through the front of the amp, and a Lexicon for time and modulation effects through the loop.
Brent
