How can I tell if her is the direct or indirect object in a sentence like, I waited 2 hours for her. Or I waited for her for 2 hours.

In general, an object is direct when there's no preposition between it and the verb, and indirect if it comes after a preposition. But, we have to be careful here as this rule has a few 'gotchas' to be aware of. Prepositions 'disappear' in some arrangements of the words sentences, so we need to make sure we're looking at the right form first.

Simple examples (English):

I rock! (intransitive - no object)

I rock the boat. (transitive, direct)
No preposition between the verb and the object.

I give flowers to my mum. (transitive, direct and indirect)
Here the preposition 'to' comes between 'flowers' and 'my mum'. 'Flowers' is a direct object and 'my mum' is indirect. In a sense, the verb acts directly on the 'flowers' and the indirect object "receives" the action. Notice that we can move the indirect object straight after the verb though and the preposition vanishes: I give my mum flowers. Now how do we tell? If we can ask a question about this sentence that starts with the preposition: To whom did I give flowers? The answer tells us the indirect object: My mum. Notice, we can't force a preposition into a question about the boat though: Who rocked the boat? I did. Therefore the boat is a direct object.

So, in your specific case, there's a preposition, and we also can ask:
For whom did you wait 2 hours?
Answer: her.
Therefore 'her' is an indirect object. 

Gotchas:

1. Whether the object is direct or indirect in an English sentence is no guarantee that the Spanish will be the same. Some verbs in Spanish take indirect objects where in English they're direct and vice versa. It's useful to understand the English as it helps understand some grammar concepts but ultimately you need to know what the structure of Spanish verb (look up, or just observe how it's used).

2. It's not always very easy to tell whether a preposition (in, on, up, down, to, from etc. in English | de, como, para, a etc,) is genuinely playing the role of a preposition, or whether it is, in fact, part of a 'prepositional verb'. English is chock full of verbs like this, where the preposition is attached to verb and its meaning, and is a 'particle' rather a preposition. Consider:

I go up the ladder. ('the ladder' is an indirect object of the verb 'to go'. Can we a sensible question starting with up? Yes. Up what do I go?  Ans: the ladder => indirect object)

I chop up parsley. ('to chop up' is the verb. 'Up' is not a preposition here, it's a particle of the verb so parsley is actually a direct object, not an indirect object in this sentence. Can we ask a sensible question starting with up here? Up what do I chop? Ah! This makes no sense, so here although there's a preposition word, we can see it's actually a particle in a prepositional verb.)

Now, all of this is helpful to understand these concepts in our mother tongue, but we need to apply these ideas to Spanish. The main reason we need to care about whether objects are direct or indirect is to know what pronouns we need to use when we're replacing the nouns with pronouns like lo, la, los, las, les etc.

So, next step is to read our lessons on Spanish direct object pronouns and Spanish indirect object pronouns. Also here's a useful list of Common Spanish Prepositions.

Hope that helps!