Floating Bridge Height For New Build, And A Saddle Question.

[j. pierce]

Calculating my neck angle for a build using this bridge. So I need to measure the height of the bridge. However, I don't have much experience with trems like this - from the diagrams I've seen in the papers that come with it, (and the guitars with similar bridges hanging on the wall at the guitar shop) it appears that the whole trem should be floating slightly above the surface of the guitar - is this true? How much? I assume I could recess this if I wanted a cleaner look?

Also, to get my calipers around the thing to measure the bridge height on it's own, I removed the saddles (so I could take off the trem block). Not paying attention, I guess, I didn't realize until after the fact that two of the saddles are shorter than the other four, and don't know which ones they were. I assume that's to allow moving them back further for intonation purposes? So that would probably mean they go on the low E and A?