I have been learning a lot of songs as of late that aren't in standard tuning but Drop D to C# and C tunings. If I have my guitar setup at a shop what should I have them set the intonation at. I plan I putting on some higher gauge strings to handle the drop tuning. Also should I have them set the string height for drop tunings so there is no buzz at lower tunings or string height for standard?

How should I get it set up?
Just tell them when you take it in that you prefer to play in drop tunings and they should be able to set it up appropriately for you. It usually works for me, it comes back out the same tuning it went in