I've taken this approach, as well. Given Google's rather complete lack of individual customer support, I do not relish the idea of trying to get a name transferred away from their registrar, in the event I need to.
I don't have any particular experiences with doing this; rather, I'm just being pre-emptively cautious.
You have to email support and they give you a token which you push into a slot that drops a ball that rolls down a chute, lighting a candle which pops a balloon and so on. I don't recall the details, but you can find people who have done it by Googling for it.
A reseller or partner with enom.com ... at $10 a domain without having the need to configure anything to Google Apps. It is pretty decent. Domain alone purchases alone without coupons/discounts are starting to cost more than $12 these days.
https://google.com/a/cpanel/domain/new
$10.
The advantage is they come all easily configured for Google Apps usage.