The 990's output side is straightforward. There would be five analog cables between the 990 and 7125, five speaker cables from the 7125 to the MMG's and MMGC, andn one analog cable from the 990 to the LFM-1 Compact.
The source side offers more options, so we'll start with video. What does the HD DVR offer for outputs? If the best it has is component video, I'd recommend connecting it to the 990 and the 990 to the Sony with two component video cables. If it offers HDMI and you think your DVD player will eventually offer the same, you could use a pair of HDMI-to-DVI cables to connect HD DVR to 990 to Sony. This would allow you to add a third HDMI-to-DVI cable for connecting the DVD player to the 990, thus letting you leave the Sony on a single HDMI input all the time. If you did this, however, you'll need to connect the 990 to the Sony with at least a composite video cable so you can get access to the 990's setup menu (s-video and component monitor outputs would also suffice for this, which is why you wouldn't need to worry about it in the first scenario).
Audio will be via a digital audio connection. The HD DVR probably has an optical output, although it may have coaxial (or both). You'll use that to get audio into the 990. The same will be true for whatever DVD player you add.
The component, DVI, optical, and coaxial inputs on the 990 are all assignable to any input, so you just need to make note of which you connect them to. There is a chart in the 990's manual that will help with that. Then you can use that information to configure the two video inputs you use for the DVR and DVD (presumably the "DVD" input for the DVD player and the "VIDEO1" input for the DVR).