How do I claim a deposit on a variation?

Open the draft claim. Every variation on the job is on it, with or without a figure.
The percentage box against a variation works like the box on a contract line. It is how far the work has got in total, not only this month.
On a variation the builder approved, the percentage claims that share of the approved amount.
On a variation they have not decided, a figure claims that much on account. The line says on its face that it is not yet approved, so they see what you ask for.
An empty box is not the same as nought. Empty leaves the variation to what its status implies. Nought asks to claim nothing on it.

Worth knowing

Some variations carry nothing on a claim, and no figure changes that: one that is knocked back, one that is dropped, or one whose notice window closed with nothing sent. Those are entitlements, not open decisions, and the claim says so on the line.