Yes, you can save up skill points and spend several at once, doing things like going from, oh, athletics +2 and rapport +1 to athletics +3, rapport +2, and survival +1 (or whatever). While I'd allow bringing a skill directly from +0 to +3, you'd need a good excuse; months of down time spent exercising for endurance or might, similar amount of time training for most skills, or you could always cheat and have a faerie drop knowledge into your brain or the like... but that last gives me plot hooks...
However, I find the requirement of maintaining skill stacks during play to be overly restrictive; my houserule is as follows:
* If your skill set follows the stacking rules, you may buy up any skill by one point. (Still subject to normal skill cap, of course.)
* If your skill set does not follow the stacking rules, you must buy up skills in a way that reduces the deficit cost of the "holes" in your stack.
So, for an example, say your skill stack started at
4 4
3 3
2 2 2
1 1 1 1 1
That's a legal stack, so you can buy up whatever you like. For example:
4 4 4
3
2 2 2
1 1 1 1 1
Now, this skill stack has holes - it's missing two skills at +3, for a total missing value of -6. The next skill point, therefore, has to go towards moving a +2 skill to +3, since that will reduce the hole to being only worth five (a +2 skill and a +3 skill).
4 4 4
3 3
2 2
1 1 1 1 1
At this point, you've got a choice; you could buy a skill from +1 to +2, reducing the hole from -5 to -3, or you could buy a skill from +2 to +3, reducing the hole to -4.
And so on and so forth.