One thing to keep in mind: if any of your mods are involved in the 'regular' maintenance, chances are the dealer won't touch them - and you should probably tell them not to. Just as an easy example: if you have an intake other than stock, they won't replace the air filter if that's included in your regular maintenance. That would also apply to your muffler bearing if you have a CBE. I always tell them about any mods that might be involved in regular maintenance just so they a) don't mess with them and b) don't charge me for something they didn't do.
You'll find that a lot of techs will ask you about stuff you've done - chances are they're car guys too. If you're cool with them, they'll be cool with you. I had a guy at one dealership and he was the only one who worked on my car - he knew my mods and watched out for me and went to bat for me when the SM tried to deny a couple of things (claiming my upgraded AMG swaybars caused a shock to fail for one). When my modded overdrive pulley shattered and drove the wooduff key through the timing chain...well...that was a different matter...
