Gross salary - before deduction of any epf, socso, pcb etc.
Nett salary - after compulsory deductions, your "take home" pay.

In salary column its always based on Gross Salary negotiation.

Whether to mention allowance, it depends on the allowance you're getting is based on a fixed monthly allowance (subject to income tax deduction) or monthly allowance like Phone, Parking etc which some companies require receipt to claim.