One proposal, three alternatives at different price points — but the deposit should be different on each. You can set that per-alternative.
Finding Your Proposal
Sales → Proposals
Locate the proposal, or search for the title, client name, or invoice number in the global search bar.
Changing the Deposit
Open the proposal.
Click the Invoice tab on the alternative you want to change.
Click the 3-dot menu next to the deposit line.
On the deposit edit screen, choose whether to adjust the deposit for all proposal alternatives, or just this one.
