You can definitely do it yourself.
Go to the USCIS website and download the I-131 package. The only thing is that you have to prove your status...so you need to have the I-485 receipt notice. That shouldn't be a problem, though I have heard of some companies not giving the notices out. Other than that, the form is very straightforward...and if you have any problems, just post on one of these boards!
I can't tell you about my wife's second application, as we only just sent it in. She had an H4 anyhow, so the AP was really not essential...it really wasn't that much of a concern that they basically lost it in the system. But for some, it could be!