I really believe that everything needs to have a place. I find that drawer organizers really help keep drawers organized. Not only are these in my office, they are also in the kitchen.
When I pay bills, I have an in-basket and an out-basket. The in-basket are bills that are waiting to be paid. Once they are paid, they get moved to the out-basket. Anything in the out-basket is ready to be filed.
I pay bills once a week. This is the easiest for me. I also pay almost everything online.
I keep a shredder next to the desk in my office.
For the longest time I saved manuals in my file cabinet (a nice wooden, two-drawer cabinet). Well, I've run out of room and needed some place else to put my manuals.
What I did isn't pretty, but it works. I got a large shoe box, and stuck all the manuals in them. I labeled the shoe box "Manuals". I taped a sheet of notebook paper on the top and wrote what manuals were in it. The shoe box is on a shelf in my basement.
This works for me because I almost NEVER need to use the manuals I have. However, I'm afraid to throw them away because some day one of those manuals might come in handy.
There are a few other options. If you have a large file cabinet, you could have file folders for manuals. If you didn't want them to each have their own file folder, you could classify them by rooms or by category. Another option is to have a large binder and put each manual in a page protector.