As a quick side note, just in case you weren’t aware, it is actually possible to budget fortnightly in Goodbudget (how to change your budget period). There are definitely people who are paid fortnightly who prefer to budget monthly, but just in case you (or anyone else who comes across this later) didn’t know this was an option, I wanted to make sure to say it.
As for your direct question – if you’re on a Monthly budget period and you set your Envelopes to Fill to the “monthly budgeted amount”, they will do just that, and Fill the full monthly budgeted amount of the Envelope. This is true even if the recurrence of the Fill itself is set to be fortnightly.
This is “one of those things” in Goodbudget where there’s not necessarily one way of doing things, because the “best” way to do something is the way that makes most sense to you. But I will say that a lot of the people who are paid fortnightly or semi-monthly who also budget to the full month don’t Fill their Envelopes every paycheck, and instead let their income accrue in Unallocated to be used to Fill their Envelopes once per month (usually on the first). (I’m also a little biased, because this is how I personally budget lol)