What is the most efficient way to use additional incubators?

The general idea is to use the infinite incubator as often as possible.

Imagine you have one 10km egg, five 2km eggs and 2 incubators (one infinite and one with limited number of uses). There are 2 ways to hatch these eggs:

• use infinite incubator 5 times for 2km eggs and limited one once for 10km egg
• use limited one 5 times for 2km eggs (you have to a buy second one) and infinite once for 10km egg

Hatching eggs both ways will take you 10kms, but the first way will consume only 1 charge unlike the second one that will consume 5 charges.

They expire when used 3 times regardless of the egg. So basically you only have two options:

• Hatch everything with anything:
  • Fast and expensive due to incubators expiring faster.
  • Good for mass hatching to increase chances for 10 km eggs.
  • Just make sure you don't hatch 2 km eggs with a limited incubator when your unlimited one is still available. Use that one first.
    
• Hatch 2 km eggs only with the unlimited incubator:
  • This saves incubator time, but eggs are hatched slower.
  • Better chances to hatch decent Pokémon due to the nature of sitting on more 5 km eggs.

Both ways have their pros and cons.

I don't hatch 2 km eggs with limited incubators (and with the unlimited one only 2 km eggs to make room for new eggs for a 10 km chance), because they're just too rare to waste them on Pidgeys.
If you're aiming for 10 km eggs and you have enough Pokéstops around to refill your egg collection it's better to use your incubators for all kind of eggs, preferably 2 km eggs due to their faster hatch time. This is of course more expensive, but a lot faster as well.

I always use it for the eggs that require the highest km to hatch.

Think of it this way, let's say you walk 30 km while always having eggs in your incubators. Your unlimited incubator gives you 30 km of "hatch-distance" during that time, no matter which eggs you put into it.

If you use the limited incubator 3 times for 2 km eggs, it'll be gone after 6 km, giving you only 6 km hatch-distance. if you use it for 3 10 km eggs, it'll last 5 times as long, giving you 30 km hatch-distance. So that would be more value for your money.