There should not be any difference in assigning a prepayment invoice to your fixed asset compared to a ordinary invoice.
So as long as the prepayment invoice amount should be a part of the fixed assets value and included in the bases of depreciation you can post it like any other fixed asset invoice.
If you are not invoiced for your prepayment you will have to use a journal to post it manually
Debet your asset and credit your prepayment vendor account or G/L account.
