This is exactly what my wife and I do. Each an account with 800K in, and a joint account for day to day living. At extension time, we take 100 Baht out of the two 800K accounts so they can see that between the last extension and the new one, there have been no other transactions.
The last couple of times we have done our annual renewal (in Phuket) our passports have come back with 90 day reports stapled in them, even though we have not been in the country for anywhere near 90 days.
My wife and I (separate accounts) each transferred a small amount, just to make sure everything was correct, and then we transferred the rest, but there is no rule as long as the full amount is there by the required date.