Logic might dictate that the simplest approach would be to input your “expenditure” estimate ex-VAT.
Then when a VAT qualifying invoice is received - the VAT is reclaimed. It’s a zero sum.
There may be some bizarre, illogical, long winded and expense incurring government accounting rule to the contrary (if it is logical to the sane mind it’s almost guaranteed to have been balls about with by the civil service) but the sensible approach would seem to be to isolate out your VAT from the budget since it is zero sum - spend / reclaim.