Before instant top-ups were introduced, you had to enter your unique reference number when doing a bank transfer so deposits would land in the right Freetrade account.
I expect these reference numbers still exist and you can still top up this way, but I’ve not one so in a while. Perhaps Freetrade support could find your reference number so you can fill in the standing order?
I have a regular monthly standing order and it goes in fine to my ISA. I then top up if I have any spare cash through the app top up facility via my Monzo acc.