If I understand your sentence correctly, you want to ask how many pieces you are to enter in the "negative stock" field on your inventory software. To use your wording as much as possible, your sentence should be:
What is the total number of pieces that go in negative stock?
OR more simply: How many pieces go in negative stock?
If the sentence is asking how many pieces are ALREADY in negative stock, you would simply ask,
How many pieces are in negative stock?
OR: What is the total number of pieces in negative stock?
1) How many total pieces are in negative stock? / What is the total no of pieces in negative stock? (How many pieces are already in negative stock now.)
2) How many pieces go into negative stock? / What is the total no of pieces that go into negative stock? (How many pieces are put into negative stock on a regular basis or as a result of a previous action.)
3) How many pieces are going into negative stock? / What is the total no of pieces going into negative stock? (How many pieces are being put into negative stock at this time.)
The point is that the meaning is confusing because the grammar in both of your original sentences is wrong. You cannot use an auxiliary verb before go/goes because go/goes is Simple Present, used when asking about a generalization, fact or routine. If you want to know what someone is going to do at this specific time, you should use the Progressive tense.
Also, you cannot use "How many number". You can use "How many pieces" or "What is the number".