to get a "nice" tone in general, those kinda heard on cd by our favourite rock dude, the main thing is not tweaking on the pedal, but the amp(speaker size, amp characteristic etc)
If you are using a practise amp or similar and using those gainy pedals like mt2, it will be hard to get much usable sound other than the fizzy and frying chicken harsh thin sounding sounds( unless thats the sound which some might prefer thou)
anyway, for tweaking pedals, theres no fixed method. A lot depend on what the player wanna hear and how it is, in a band setting, jamming together. We can spend lotsa time tweaking in our bedroom/house to get the most killer tone known to man or jamming with backing tracks/stereo player etc , but if never play in a live band context, there will be many things which we will never noticed being in our own room or headphone.
for the chrous thingy, think of it in this way
1) Do you prefer the chorus to process your clean sound first then going into the distortion
or
2) Do you prefer having the distortion signal going into the chorus then to the amp
Both sounds different and if you not sure what you like, the easiest way to find out, is to get a chorus pedal, try out the above 2 ways and listen to hear which one you prefer.
In term of pedals playing, other than reading or finding out about what other people are doing, the more important thing is to learn how to listen to sound and finding the right context to insert the tone, for the music we are doing. Unfortunately, it wont be something that can be picked up from forums in a short while. Need to spend time playing, listening, reading and then more playing, listening to find out whether the info read coincide with what we are playing/hearing or contradict it.
imho