TL;DR what does している mean, or what can it mean given various circumstances?
What are its limits of use?

I am confused on the meaning of the verb する plus the ている ending. I know する has
many meanings such as "to do" or "to wear." However, I am always confused how
to interpret している; it seems a little weird. It can be used to mean to have or
not to have, as in a part-time job (いいえ、アルバイトをしていません). I think it can be used
to mean "wearing," such as どの人が黒いTシャツをしていますか, but since I made this sentence I
am not sure. It can also refer to something you are doing, like いま、なにをしていますか.

Since I do not know exactly what しています refers to I find it hard to use in
various situations and sentences. How do you personally interpret and make
sense of しています as the verb する plus the ている ending in sentences? How can you
use しています if it has so many meanings, and how do you know when it can be used
and when it does not make sense?

In the genki textbook, する just means "to do," so maybe that is where the
confusion caused by its many meanings is coming from for me...
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verbs
What does しています mean?
Unfortunately, Genki's job is to ease you into Japanese. To get you started.
It can't and won't teach you everything, so take what Genki teaches you at
face value and not as absolute law. There is a high chance you'll come across
a lot of things where Genki has said "this means X" and in the real world you
find out it means or can be used a million different ways kind of like する.

Anyway, you are right. している is just the ている form of する. And you are also right
that する has many different meanings. A lot more than just the "to do" meaning
Genki has taught you.

している is the same verb just in a different tense. I don't think you should give
it any more special treatment / meaning than some other ている form of a verb. I
understand that する covers a lot of different meanings, but I think that is
more of an overall sentence context problem and having to pick / interpret the
proper meaning more than anything else when translating to English.

That being said, in my option, I think any ている form should be thought of as
"in the state of the verb" instead of just the simple "ing" explanation that
many resources will give you. They do this because it's easier to understand
when you're first learning Japanese and are coming from an English speaking
background. But it's really just being in a state of the verb. Famous example:
死んでいる. This doesn't mean "dying" it means "in the state of to die" AKA "dead".

Like I said before, I don't think している is an exception to this. Taking your
example:

> いいえ、アルバイトをしていません

I read this literally as:

> No, I am not in the state of to do a part time job

But that sounds odd in English. So cleaning it up we get:

> No, I'm not doing a part time job.

OR alternatively

> No, I don't have a part time job.

As you can see here, している can mean "doing" or "having" from an English
standpoint. Things like this can easily add to the confusion of what does する /
している actually mean when you try to nail a English definition down when one
size really doesn't fit all. So you have to leave it open to interpretation a
bit when translating from Japanese to English.
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しています is a combination of する and -ている (or -ています in polite form), both of which
are difficult topics.

### Meaning of する

You seem to understand this, but [する has many
meanings](https://jisho.org/word/%E7%82%BA%E3%82%8B). Basic verbs like する, やる,
とる, かける, みる and so on have many possible translations, and you cannot
understand them just by thinking of a single translation. The same goes with
English; you may think _take_ is an easy verb, but to a foreigner, _take_ is a
really difficult verb that [must be translated in dozens of different
ways](https://dictionary.goo.ne.jp/word/en/take/). You have to accept such a
fact and learn each usage one by one.

### Meaning of -ている/-ています

Fortunately, the -ている ending basically has only three meanings:

  1. is doing now (progressive)
  2. has done (perfective)
  3. do on a regular basis (habitual)

For details, please read these two questions: [When is Vている the continuation
of action and when is it the continuation of
state?](https://japanese.stackexchange.com/q/3122/5010) and [Habitual
aspect](https://japanese.stackexchange.com/q/11925/5010)

For example, 部屋の掃除を **しています** is a sentence that, depending on the context,
means:

  1. I am cleaning the room (now)
  2. I have cleaned the room (so the room is already clean)
  3. I clean this room (regularly) / My job is to clean the room

今何をしていますか only means "What are you doing now" because it clearly says 今
("now"), but 何をしていますか by itself can have a habitual meaning, "What do you do
(as an occupation)?".

Similarly, アルバイトをしていません is _usually_ habitual; it typically means "I am not a
part-time worker" rather than "I am not working part-time (right now)".

指輪をしています is _usually_ perfective; it describes the state of having a ring on
your finger, because wearing a ring is usually an instant process.
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