Thanks to some recent changes in Manager (see [16.7.73] Categorization against customer and supplier accounts more intuitive), this is easier than it used to be, no longer requiring an Advanced deposits account.
Just Spend Money from a cash account and allocate the transaction to Accounts payable. When the subsidiary account box appears, select the supplier. Do not enter an invoice, because you do not officially have one yet. Enter the deposit amount.
This will create or add to the Supplier credits asset account, and Manager will know which supplier the credit is with. When the supplier invoices you, enter the purchase invoice and Manager will automatically apply the deposit to the invoice, zeroing out Supplier credits (unless there were additional deposits) and show the balance due.
Notice that nothing is entered into any inventory account until the purchase invoice arrives. Manager does not yet have the ability to track inventory items on order versus in production versus in stock. When the warehousing module rolls out, it will.