One thing to remember when you are talking to someone who deals with or is focused on the general public and not someone coming from the sports context -- they probably have never seen any of the advice of the type that comes from a sports / fitness context. I dont' know for sure, but doesn't the maker of the "Food Pyramid" and the old "4 food groups" recommend ridiculous high carbs?? I wonder if any of this has been adjusted to take into consideration the typical sedentary lifestyle??
Anyway, dont' take advice from people who dont' come from the sports industry. I think you will also get bullshit advice from people who are "weight management counselors" like with Jenny Craig, etc. Most of those organizations dont' include fitness / training as a fundamental part of their programs. And within the sports industry, take advice from people selling stuff (e.g. the GNC guy) with a grain of salt. They are all biased.
You will probably never get the exact same advice from two different trainers or anyone who claims to be an expert in the sports industry either. But the basics should be there. That has been my biggest complaint about trying to educate myself and also to find a trainer to help me with competition. I paid a guy a shitload of money and got screwed and have been spending a year trying to get the extra bodyfat off as a result. So, its pretty obvious to me that its up to me to collect lots of info, cull thru it and pull out what I believe or have proven to myself is best for me.
I know what you mean about cracking knees on squats, and I am also very careful with my form. I might recommend doing some stretching or a little warming up before going into squats. My knees crack when I get up and walk after sitting at my desk for a few hours. But definitely be very careful w/ your knees. Its like getting tendonitis in your elbows -- you don't really notice it until you "need" those joints. Then it can hurt like a BIATCH! And something about those non-obvious, but always nagging pains - they NEVER seem to go away and you can't ever seem to fix them either.