I don't have a preference. Invoices remove the worry that I misdirected the payment but typically I just copy paste the email address it so I usually feel worry free enough.
I guess manual/invoice mostly applies to dealers? Almost all the doll companies I've bought from have automatically directed me to PayPal for payment. As for dealers I've used, namely Clover-Singing, Legend Doll and Dolk, they actually advise you to wait for their invoice. In fact, Clover-Singing doesn't allow manual payments now because they had problems with PayPal suspending them for a while for receiving 'suspicious' payments. Anyway, I usually prefer to wait for the dealers to invoice me, in case they suddenly find out that something is out of stock and they are unable to order it for me. The out of stock situation actually happened with Dolk, they had a doll I wanted during one of their 'in stock, fast shipping' sale. I was a little wary about ordering from them (due to all the horror stories and I personally wasn't too pleased with an order I made with them before) but it was a grail doll I really really wanted and he wasn't available anywhere else. Since he was 'in stock', I decided to take a chance. However, while waiting for an invoice from Dolk, they suddenly cancelled my order and said something about how they apparently made an error with the listing and they did not actually have that doll... It was certainly disappointing but I'm also very glad that I waited for the invoice before paying!
I personally prefer invoicing because it's like a physical reminder I can see while manual there is a chance of forgetting.