When I set up my speakers.. i first use the Auto set up from the 990. It's pretty close I have found for proper levels.
When i want to set things up manually. I use a Discwasher digital set up disc. It has a seperate set up set of tones for DD and for DTS. Giving me the reason for the different set ups required for each.
Yes in theory, you should only have to set up your speaker one time.. and it should be fine for all sources and decoding of those sources. But as mentioned earlier, I find that DTS seems to run a bit on the "hot" side.. making my set up setting slightly different between DD and DTS.
Anyway, lets get past that.
I have my center located just below my TV. It's a tube TV. It's to large and heavy (30lbs) to be place on top of the TV.
I have never heard anyone mention that it's not a good idea to have your center timbre match your mains. I won't agrue that is't not a good idea.. but I have trouble accepting it as a good thing.
To obtain a seemless panning of the front soundstage, you really do need to timbre match all three front speaker. Level wise, yes you can set them all to the proper levels.. but mis-matched center and fronts.. and you'll notice a definate out of sync front soundstage.