I'm setting £20.50 aside for this year's fees (was £25 but I've incurred 3x dealing charges at £1.50 due to carelessness) which I think is a bit conservative but should allow for some growth. I will then set aside slight more next year, etc. (Based on a £5k investment including the bonus)

Your shares will pay dividends?

The easiest thing is maybe to just retain a cash float of a tenner or so which is always going to be higher than the next quarterly £7.50 charge. Or if investing all at the beginning of a tax year, so you need to "survive" longer than a quarter, retain enough to cover the fee with a buffer to spare until you get to the next tax year and can top it up again.

Retaining 0.25% of whatever you just invested is potentially flawed as by the time you get to year two you are investing what you just invested but you're also continuing to invest what you had invested the previous year and the charge is on the whole balance rather than what you just invested right now, so you'll need a greater holdback than what you'd just get by holding back 0.25% on the new money being invested at that point.

The lost performance from having even £30 idle for half a tax year is only a pound or so (assuming 6-7% returns) so leaving money on hand for fees isnt going to destroy your performance. As you say, there will always be a little bit left over naturally from each purchase due to your purchases not being able to buy fractional shares, but erring on the side of caution probably isn't going to hurt you too much so a complicated plan is probably unnecessary. Just project an estimated "worst case scenario" for fees (based on best case scenario for investment growth, and knowing there's a cap after £12k) and hold some money back based on when you next think you'll get around to funding the account again.

Better to hold money back than be forced to sell to get cash (or worse, for them to sell at their discretion at a high charge rate), so some over-caution is probably ok.

Having incoming dividends will help (which is how my mum finances her fees on a tiny sipp) but the divs won't arrive evenly through the year so need to be combined with some sort of cash float.