You are going about it the wrong way
, probably because like most decent recorders the Pioneer offers multiple methods to accomplish the same task but the instruction manual is none too good explaining any of them. Years ago I settled on using Pioneers exclusively, based on the fact they have the most robust editing system out there. Trust me, Pio editing works very well once you figure out the process.
The first thing you need to do on a 650 (or any hard drive equipped recorder) is get out of the habit of recording directly to DVDs: if you are doing that, stop. The whole point of the hard drive is that its a limitless "scratch drive" for editing and offers more editing capability than DVD-direct. Only burn to DVD after you've completely set up the recording on your hard drive.
Second, like most decks that offer auto-chapter marks on the hard drive, this "auto" function is more trouble than its worth and should be disabled: turn it off by going into home menu/disc menu while in HDD mode. Going forward, each recording made on the 650 hard drive will then go down in one continuous block. When you are ready to edit out commercials, do the following:
Highlight the title in the navigator window, press the right arrow button to bring up the "edit" menu, and from that menu choose "erase section". That will bring up a complete editing screen, with a preview window and timeline bar. Here you select a start frame, scan ahead to an end frame, and approve the edit. You will see a preview of the edit, and be given a chance to modify the start and end points. When given final approval, the commercial break will be removed and a chapter mark will be inserted at the edit point (these edit point chapter marks cannot be deleted). You can continue in this editing mode all the way thru a title until you have removed all the commercials, then exit back to the navigator by hitting the return key.
Some people who have used older recorders prefer the method suggested by kjbawc, in which you bookmark the beginning and end of each commercial break in "chapter edit" mode, then delete each chapter which consists of a commercial break. You do this by entering the navigator>edit>chapter edit screen. In this screen you can also insert your own manual chapter marker points anywhere you like, or remove them. You have the same fine control here as you do in the Erase Section mode: simply put the machine into pause as a commercial break starts, then use the step-frame rocker button to locate the exact beginning point. Mark it as a chapter, then do the same at the end of the break. Then just delete that "chapter".
NEVER use the "navigator>edit>divide" function unless you specifically want to divide a title into separate smaller titles (say for example, you recorded a mini-marathon of your favorite show that ran four hours- you'd use the divide function to break up that recording into the individual shows).
Note that all the above editing tasks, when accessed directly from the navigator window, are irreversible, can't be "undone", and are therefore "destructive" to the original recording. A lot of people are afraid to make a mistake they can't undo, and for them there is another option called the "copy list". You enter this mode by going into the home menu and selecting "copy" and then "HDD to DVD". A window will open allowing you to select which titles on the HDD you'd like to add to the current "copy list". Once those titles are in the copy list, you can do whatever edits you want and they WILL NOT affect the original recording, which remains untouched on the main HDD nav system. The edited version will be dubbed to a DVD you create. If you make a mistake before dubbing, you can just delete the botched title from the "copy list" and add the original title back in again.
This is easier to do than describe, and its illustrated reasonably well in the manual, but you kinda have to study it a bit. There are a few subtle differences between "direct edit" and "copy list edit" modes, which are covered in the manual (such as how to activate the editing options on a title in the "copy list": instead of right arrow, you highlight the title and press the "enter" button to bring up the edit options. You scroll down those options past "cancel" to bring up a second screen with more options, such as combining titles.)
One last tip: each time you open an editing session, the recorder will ask if you want "video compatible" editing or "frame accurate" editing. There is disagreement among owners which option is preferable: supposedly the "frame accurate" mode only works on the hard drive, and those "perfect" edit points may shift slightly when copied to a DVD because DVD authoring requires "video mode" edits to be made on key frames in the MPEG2 stream. Many times there is no shift, and "frame accurate" edits are unchanged during DVD transfer, but if you want an absolute guarantee the edits will carry over exactly then you should do them in the default "video compatible" mode. This mode forces your edit point selections to roll over to the closest key frame, usually within a half-second of your chosen frame. Slightly annoying but generally no big deal, the recorder gives you an accurate indication, and it ensures "what you see is what you get" results.