Well, there is certainly a lot of "meta-designing" you can do before even starting the map in Hammer. Most of it having to do of course with what you're designing. In Dystopia you're going to want to avoid a chokepoint that can be spammed with grenades and such too much, in TF2 you're going to try and implement some nice turret spots for engineers, etc. A lot of very minor things someone wouldn't notice can make a huge deal, for example aligning spawnpoints the wrong way and making players have to turn around every time they spawn.
I tend to be a perfectionist with numbers and lining up textures/geometry, which can be both good and bad. Although sometimes it can feel like a waste of time, it can also save your ass and make design changes a lot easier (i.e. one small example, in the EU3 area in undermine the ceiling is 32x32 unit squares aligned the to grid, and in the version coming in v1.2 there's a new vent exiting from the roof there with a dimension of 128x128 - since it all adds up I didn't even have to realign any textures or anything). It can especially save your ass with geometry since a wall being even one unit off can cause a leak in your map (generally the best thing to do with geometry is try and use as big a snap-to-grid value as possible, don't ever use 1 unit snap to make big pieces of geometry or turn off snap to grid).
I will say that getting proportion right is definitely a "feel" thing when starting a map rather than a math thing. One thing I'll do is make a bunch of "props" (basically model detail in hammer) and use the player models as the graphic - they'll be in the default arms-outstretched pose, but this way you can easily see how they line up with the geometry. Obviously this is a non-issue for a map for like HL2 single player since you can just use NPCs but for multiplayer maps it's a pretty useful method for assisting in getting proportion right.
Sorry for random rambling, just trying to spew out any tips I can think of.
