I started out by doing extract recipes, which I would think is the next step up from the "all in One" kit. I was able to find all the ingredients at my Local Home Brew Store and, following the teachings of John Palmer's How to Brew, I was (and am) able to make a decent brew. I did not think that this process was hard at all. If you can keep things clean and neat, you can tell time, and you can boil water, you should be all set I am now doing extract w/steeping grains, and doing my first partial mash next time I brew, in advance of going All Grain.
As for the hops question, there are some who filter them out after the boil, some who leave them in. Were these the hops from the boil, or were you adding more? In either case, I don't think that it is a problem. I have added hops to my secondary and it worked out fine. I just made sure to bring as little of them as possible when I transferred to the bottling bucket. Next time, I think I might transfer them to another carboy a day or two in advance, to help get more out.