The round-up idea is just a mental trick to help people donate using a 'keep the change' mentality, so if that works with your customers then go for it. Tax wise, a donation is a donation as long as you aren't passing through the deduction to your customers. So, you could ask for people to 'round up to the nearest dollar', you could ask them if they would like to 'add a dollar', or just put a percent of every purchase as a donation.
Unless you are going to administer the funds in some special way or pass-through the tax benefit (which you really can't do) there is no need to even maintain the special account. As you do your bookeeping just keep track of how much $$ is allocated to charitable donation, then give it away when you are ready. A separate account may be convenient, but may not be depending on how you want to handle it.
"The fewer our wants, the nearer we resemble the gods." — Socrates