Weight training help needed

Ok.. so I've been doing weight machines for over a month.  One of the trainers saw my weights, reps, and such and told me I was doing too many reps with too low of a weight.  For example, I was doing 90lbs on one machine with 3 sets of 15 reps (starting at 12, working up, when reach 20 on all 3 sets, go up 5 lbs and start at 12, etc.) So he tells me to do a max push for one rep, then work at 65% of that level for 3 sets of 8, working to 12, then moving up 1/2 pound.  So that 90lb machine moved to 115. Well, my arms are fine... a bit sore the next day, but fine.  But in the process, I seem to have pissed off my knees.  Specifically, the sides.  Walking was painful, jogging was downright challenging, and steps are still excrutiating (sp).  I asked which of the machines was the culprit and knocked my weights down.  This was on Tuesday.  Last leg weight day was Thursday, with a couch-5k session on Friday.. and I still hurt.  I rested yesterday and will do so again today to try and help healing. So, any suggestions? I don't want to stop the couch-5k program (and only do it 3x/wk).  Should I knock my weights back down to where I was?  Knock them halfway between the two points?  Give my knees a few more days before doing lower body again?  Or keep going, but maybe with a brace (and hey, do they work and are they available for my fat knees?) Sorry to ask so many questions, but with this injury, I feel less confident in the trainers at the Y (especially since this gentleman was in his 70's.. wasn't one of the trainers that push massive bodybuilding, works primarily with the seniors, etc.)

First of all the pain in the knee could be tightness in the IT band which runs the length of your thy.  It it IS tight, it can cause severe pain on the side of the knee and a little behind the knee.  Start with this stretch to see if it helps. http://www.rice.edu/~jenky/sports/itband.html As far as the reps per set thing goes, it really depends on your goals.  When I am gearing up for my marathon season, I will do reps in the 20's to 30.  It is for the endurence.   If I am looking to build muscle, I will do lower reps of 4 to 8 at a high weight.   My typical routine after a long layoff has me starting at 3 sets of 8 at a light to moderate weight for about the first two weeks.  That helps keep the intense soreness away.   It sounds to me as if your program was working for you but his sounds pretty text book also.  See if you can't get that knee pain to go away without having to give up the couch to 5K.  Good luck