I have a question concerning setting deck height.

Do you first need to know what the cc of your combustion chamber is so you can work back to what you want for compression ratio which in turn will establish your deck height?

or what is the proper process to follow?

I think that compression ratio is the relationship between "swept" volume and "unswept" volume. Unless you are willing to change the size and volume of the combustion chamber, I think it would be easier to adjust deck height. I think the first thing is to get all the combustion chambers equal to one another by cc ing them. Then you need to add that number to any "unswept" volume on top of the piston. Swept volume is what the piston moves from bottom dead center to top dead center, or it's displacement. As long as the piston doesn't extend into the combustion chamber ( like a dome piston on a hemi , it shouldn't be too hard to figure out. The way you phrased your question I think you already knew the answer, so yes, cc the chambers first !

Yes, you have to know the combustion chamber volume--then you decide your target Compression ratio, then enter that into the calculator like the one on CB performance (http://www.cbperformance.com/v/enginecalc.html) to find the deck height.
Buy two or three sets of shims and carefully deburr them and then measure them--I've found wide variation within a pack of shims and had to combine from two packs. Put it all together and use some clay on top of the piston to check for valve clearance--enjoy!

Not only can you change your deck height (which I prefer to keep at .040" or less), but you can fly cut the head to bring up the CR (by reducing the total volume of the chamber). If you need to lower your CR and want to keep the DH at .040" or less you can dish your pistons. If you are running AA pistons don't forget to CC the valve pocket in the piston and add it to your calculations.

If you go under .040 you need to make sure your valves will not kiss your pistons. Easy enough to do with a little clay, but you NEED to do it.

And, yeah - what everyone else said. You need to CC your heads. Also a pretty easy task.

Zach