Agree with RicF... it's a washing machine. Everything goes in together. I keep wool separate/hand wash and tend to wash whites separately but otherwise towels and non whites, running/gym/swim/bike gear all goes in together. Unless I've been away MTB'ing and have load worth of really mucky gear - obviously then I'll just bung that all in together, but otherwise I don't see the fuss.
Also, just a thought.. why would you be going onto road with the winter coming in? (i.e. XC season... grass!!, potentially icy roads... we tend to be on grass more in winter ). Keep persevering though, it's tough but great fun!!!
It depends what you are doing but generally yes, if you are doing reps on say a few hills around the area then you would do a few on each (depending on what session you/friends/club have devised) running up and jog ging back down. Do a couple at first at low intensity to ensure you are warmed up. (Perhaps an easy jog for 10-15mins prior to the session). Once you have done your allocated reps on a certain hill, just jog to the next hill. Nothing complex.