As a merchant can I set up Apple Pay to link to multiple bank accounts?
Apple Pay is a very different technology from something like Square, which would operate similarly to how you describe. You sign up as a merchant with Square and link it to your bank account.

In this situation, Square is the point-of-sale, acquirer, and merchant account all in one. And as a matter of fact, they support using Apple Pay at the payment terminal.

In a more traditional merchant situation, you have a merchant bank, which will put you on a specific processor platform, as dictated by the needs of your payment gateway and point of sale. As a merchant, you don't have any interaction with Apple at all; if you want to accept Apple Pay, you just need to make sure that your point of sale is capable of accepting NFC payments, and that this is all supported by your gateway and platform. Typically, though, you will only be interacting with your merchant bank, and they will be able to facilitate the set up of an Apple Pay-compatible POS.

So, this means that typically the funds will all be deposited into the merchant account that is linked to that point of sale. You could probably have your merchant bank set up deposits to your business checking accounts in percentages as you suggest, but there is typically a 1:1 relationship between Point-of-Sale or Payment Gateway and your merchant account.