How do internally carried IR missiles acquire a lock?
If you are referring to the Sidewinder missile, the first iteration AIM-9X did not have a requirement to be launched from internal stores, known as captive carry, but in testing it demonstrated that it could lock on after launch. This was deemed interesting enough that Raytheon got a contract for the Block II variant, which among other things adds a datalink capability so that an aircraft with the right equipment can direct the missile to where the target is located, after which it locks on with the IR sensor. This allows it to be used on the F-35, F-22 and even submarine platforms.$^1$

Block III has the same datalink capability (derived from tech developed for the AMRAAM missile) but also has increased range and an insensitive warhead that reduces possibility of accidental detonation on the ground, among other things.

A big reason why the AIM-9 series continues to be upgraded is because of its IR capability. Some countries have developed jamming technology that can interfere with the more modern AIM-120's radar tracking system.



$^1$: Raytheon AIM-9X Block II Missile Completes First Captive Carry Flight, spacewar.com, 2008