Hi Diana,
I, too, had a bit of a struggle on thinking how to incorporate online payment with my greetings cards. I thought about Google Checkout as I already had a gmail email account but discovered I couldn't sell with in multiples or other options without paying for a third party shopping cart - something, at the moment, I don't want to possibly waste money on if it all falls flat. However, you've already got paying customers so I doubt that would happen to you.
I then found out that Paypal do a 'free' simple shopping cart but for more commission. I already had a paypal account and since I am just starting out I didn't have anything to lose. I did it all myself with little to no knowledge but fairly competent computer skills and determination. I finally got it working with different size choices, multiple and personalised options. I did have a fair bit of trouble, it has to be said, but I think it might have been a bit of a Mac conflict. And to give them their due, the Paypal technical monkeys on the online discussion board help thingy were very good. Oh and, people don't need to have a paypal account and can also just use a credit card.
My cards are individually made but can be simply personalised so I set it up to do so. However, I do give the buyer the option of filling in my contact form if there are specific requests and have advised them to do so first before ordering. You can also select the option for "Ask further instructions to seller" box, (or something like that) I think it comes up on the final payment page.
I have heard lots of scare stories about Paypal not paying up etc. but until I make my first million

I'm gonna risk it before I shell out for a fancy shopping cart. Benefits of going through something like Google Checkout or Paypal rather than straight email invoicing is you don't need to worry about sharing bank details, waiting for cheques, cheques bouncing etc. and it gives people options of how to pay. I buy stuff online quite a lot (especially since I'm out in the sticks) and personally if I see a website without an online payment option I don't bother - too much hassle. That's why I decided to take the plunge.
I have seen though, on some people's sites they use Google Checkout and send an email invoice later with a Buy it Now button when everything is added up which maybe more what you're looking for. It does take longer of course but it still gives that instant access a lot of online shoppers look for and the interaction you're looking for.
That all said though, I haven't actually had any online sales as yet but it's early days and I'm working on a bit of promotion so here's hoping.
I told you I can waffle!!
Good luck with it all.
Jen.