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Not sure about Eagle, but I use designspark where hole sizes are global. you can define your own or use the defaults. just modify the global and it applies to all the pads.
I set hole sizes depending on the drill bit that way the drill bit sort of self centres as you drill.
I use a 0.8mm drill bit for standard components and 1mm drill bit for connectors. you only need to drill through fibreglass and not copper as well. works very well for me.
Brendan, I haven't heard of tinning crystals, if the copper is clean enough, you can solder easily by ensuring the copper is heated with the tip. I use the 0.8mm lead. I tin/clean component leads with a blade before soldering.
For protection, I've seen the sprays in jaycar which protect the copper but you can still solder over it.
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