I have a Sony BDP-S350 and a 2808, so you're in good company. I'd recommend doing the full 8 position Audyssey setup (use the guide linked in the first post on the 'Official Audyssey Thread'). Once you've done this, you can tweak the speaker crossovers (mine come up as 40Hz fronts and centre, but it seems to be recommended to raise this to 80Hz and leave more work for the sub to do).
You can save three presets on the 2808 ( I assume the 988 is similar?). They allow you alter channel levels, Audyssey setting (Flat, Normal, Manual or OFF), restorer settings (useful for improving low bitrate Digital TV broadcast sound in the UK and of course for iPod sound too), tone settings and main volume (plus others). You can save these prefered settings by just pressing and holding the button down (below the volume on the unit itself).
I saved one preset with the original Audyssey channel levels and other settings relevant to higher volume listening. The second setting is for lower volume TV listening with +3db on the sub and surround levels (works better at lower volume) like a preset 'loudness' control. Final memory is for listening to CDs in stereo direct mode. What I like with these settings is that they save the main volume setting too which is a useful reset tool if you need to turn the amp down to answer the phone, etc. You can also set the volume level at switch on too, which I like (incase it was set loud the last time it was turned off). Those memory settings go a long way to optimising my setup, so that I don't feel I missed out much on not getting the x2 priced 2809 model with dynamic EQ and dynamic volume (I got a really good deal on my 2808).
There's probably more, but that should get you started.
EDIT: Make sure you have your 350 set to bitstream output to get the 988 doing the decoding and you'll see that DTS-MA/Dolby True HD light come on for relevent discs.