Using a separate invoicing system tends to be the way most people go. I'm a huge fan of Hiveage myself, as the interface is clean, they have a good number of features and you can use a custom domain. That said, there are plenty of other alternatives including Freshbooks, Square and many, many more (including the host-it-yourself Pancake App -- of which I have a license that's no longer being used if anyone is interested).
I haven't tested it myself, but it might be possible, using the Client Billing function, to charge them a large amount for the first month and then adjust it down afterwords. If it can operate that way, you'd want to ensure the billed amount gets ajusted after the first charge, or else you'll have a very angry client on your hands.
I've also seen other companies that don't charge an upfront cost, just a higher monthly/yearly cost.