Personally, I would find a way to put it all on the credit card, if only for the credit card benefits ... which you may or may not have on your cards.
I know that Amex requires the entire purchase be on the card for the extended warranty to apply.
The Costco Visa card only requires a portion.
In any event, if you can call your credit card company and tell them that you want to raise the hard cap for a one time purchase at the Apple Store, I'm sure they can let that one through while keeping the hard limit in place for everywhere else.