I think its hard for many players now to appreciate just how different playing through a hard driven amp is compared to pedals or especially "amp simulators". The real thing is subtle, but distinctly different. Kind of like when you rent a movie, and you can tell it was shot on video, not film.
Good news though is that the pedals, amps and simulators available will do a really good job. For your pedal, I'd say keep the output quite high, but the amount of distortion fairly low. For amps, its finding that perfect blend of master gain/channel gain. If you keep the Master Gain really low, but roll the Channel Gain up high, the amp will over-drive, but probably too much... if so, roll back the Channel Gain and add more Master until you find the right mix. If you're working with an amp simulator, try looking for a Marshall JCM 50w preset, and play with that. You should be able to get pretty close.