There are two issues here that I'll address separately (I'll do 2 posts, since this is long): INSTEAD OF v. RATHER THAN, and parallelism with prepositions.

INSTEAD OF and RATHER THAN are not interchangeable. RATHER THAN indicates preferences, and can be used in parallel structures with nouns, modifiers, or verbs.
The company should invest in stocks rather than bonds.
I recommend eating a light snack rather than consuming a large meal before a race.

When comparing infinitives, the infinitive after RATHER THAN is used without the TO:
Jane decided to bike rather than drive to work.

INSTEAD OF suggests that one thing (or person, or action) replaced another. On the GMAT, INSTEAD OF is generally used only with NOUNS or (less frequently) with present participles. It is not used with infinitives.
I ordered tea instead of coffee.

In this sentence, we're comparing how heat is applied: either evenly over the total surface, or to a series of irregular points. We're not replacing one with the other, we're preferring one to the other. Furthermore, we're not comparing nouns, so we should use RATHER THAN.

The second issue here is parallelism. It may not seem that "evenly over the total surface" is parallel to "to a series of irregular points." But ask yourself, what are my parallel elements?
It is important that heat be applied (one way) rather than (another way).

In many cases on the GMAT, we need to use the same preposition in order to maintain parallelism.
The wounded bird is not capable of flying or of finding food.
Here, the verb CAPABLE requires the preposition TO.

In this sentence, however, the verb APPLY does not require any particular preposition. Apply heat TO something and Apply heat OVER something are both idiomatically correct. When you're looking at parallelism with prepositional phrases, it's ok to have 2 different prepositions, as long as the verb doesn't require a particular preposition.