#1
I recently bought a Bugera V55 (and also own a Marshall AVT50H), and as both of these have effects loops, I'm wondering what the difference is between using the lopp versus running your guitar to your board and then directly to the amp's input.

Thanks for the help.
I play guitar in a ska band.
Modded MIM Strat > Fender Tuner > Bugera V55HD > Custom built 2x12
#2
It depends what pedals are on your board. Most people prefer time-based effects in the loop and then wah, OD, compressor, noise gate, etc. in front. Experiment to figure out what sounds best to your ears.
#3
The difference is, that it affects the place of the units on the signal chain. Putting things in front of the amp puts them in before the preamp, so then they'll be subject to gain, EQ, etc, everything that the preamp does to modify the signal. If you put them in the loop, they'll be placed between the preamp and the poweramp, making them go to the poweramp without being subject to the same factors. There is a difference heard in the sound, but there's no right or wrong here - try placing your pedal both ways, and see which you like the best.
Gear:

Guitars: Ibanez SV5470F, Ibanez Xpt700, Fender MIM Standard Stratocaster ('04-'05), Jackson Ps-2
Ashton AG200,
Amps: ENGL E530, Bugera 6262-212,
FX: TC Electronics G-major 2, Behringer EQ700, Morley Volume / Wah