DK tanking is all about patience. There is a lot of downtime with the class right now, and you are correct for not just dumping all your runes at once. If you find yourself in that position often, then perhaps you are using rune strike when you don't have both F and U runes on cooldown? you need to rune strike when you have xBxxxx to guarantee either an F or U rune getting returned from RE procs.
One of the reasons I only recommend RE as a dps choice in my guide is that in progression tanking as a DK you want to have a DS available at all times if possible, and RE requires both FU pairs being on CD. If you are doing something other than 5 mans i'd recommend switching to RC or BT, as you don't need to game your runes in a DS-inefficient manner to maximize throughput.