The word order is likely the problem. A finite verb (conjugated part of the verb like machst) moves to the end of the sentence only in side sentences.
Weißt du, was du jetzt machst? (side sentence "machst" in last position)
Do you know, what you are doing?
The place for the finite verb in a normal main sentence is in second position. It only moves to first position in imperatives or questions.
Machst du etwas? (1. position, no question word)
Are you doing something?
However, a question word (was, warum, wie, wann, wo...) can also start a question and then the finite verb takes second position like in a usual main sentence.
Was machst du?
What are you doing?
Finally, every main or side sentence can only contain one finite verb. Additional verbs are either participles or infinitives (not conjugated). Modal verbs (sollen, dürfen, können, müssen.... should, may, can, must...) are usually combined with a full verb (normal verb), which is then moved to the end of the sentence and in infinitive (not inflected).
Was sollst du jetzt machen? sollst finite verb, machen infinitive
What are you supposed to do now?
Hmm... Yeah, I see "machen" used as "do" most often, but since it means make shouldn't it still be accepted?
Also, how do you know to use "sollst" instead of "solltest"? I saw someone say that "sollten" is more of a personal suggestion, while "sollen" is an obligation. Wouldn't "solltest" be used in that case? (Sorry... I thought I understood the difference, but when I started thinking about it I realized that that definitely isn't the case.)
You are quite right about suggestion and obligation.
The grammar answer is that "solltest" is conditional and "sollst" is plain indicative. I think in English only the conditional form survived "should".
Du solltest das machen. You should do this. (conditional)
Du sollst das machen. You have to/are supposed to/are obliged to do this. (indicative)
You can compare it to conditional forms of other modal verbs to get a feel:
Du könntest das machen. You could do this. (conditional)
Du kannst das machen. You can do this. (indicative)
Du müsstest das machen. You would have to do this. (conditional, there is no form for must)
Du musst das machen. You must do this. (indicative)
By the way: "solltest" could also be past tense instead of indicative. The forms are identical. This is not the case with the other examples.
sollst/solltest/solltest, kannst/könntest/kanntest, musst/müsstest/musstest, darfst/dürftest/durftest,
2nd person present indicative/present conditional/past tense
Here you'd likely use "noch" (still), instead of "jetzt" (now), and probably switch the modal verb to müssen as well: Was musst du (immer) noch machen?
Using "sollen" here would be more of a "What more should you still do?" (again, assuming noch) Similar, but nuanced.
Your question above would translate to me as "What should you do now?" ... perhaps as in "Ach nein, der letzte Bus fahrte ab! Was sollst du jetzt machen?"
Yes and no. Du is the informal singular you. machen - is infinitive here, the verb in its non-conjugated state. You have two verbs in this sentence. Machen is dependent of the modal verb „sollen“. In this case sollen is conjugated to „sollst“ (du - 2nd person singular ending -st), while machen remains unchanged and moves to the end of the sentence. This is a verb bracket - conjugated part in second position „sollst“ and the rest „machen“ at the end.