Can I use PayPal Micropayments together with PayPal Pro?

You can enter the PayPal Email for a separate Micropayments account in Seller Admin > Edit Profile, so all order totals under $12.00 would be paid to that account, rather than to your main PayPal Email. If you expect all your payments to be under $12.00, you can disregard that Micropayments setting and just enter the PayPal Email for your Micropayments account in Seller Admin > Edit Profile, so all your PayPal payments would be sent to that account regardless of order total.

Bear in mind your selection of PayPal Payments Standard vs. PayPal Payments Pro on that Payment Preferences screen affects the checkout options offered in your cart regardless of order total. This means if you're diverting order totals under $12 to a Micropayments account, your regular PayPal account and your Micropayments PayPal account must both be set up to use PayPal Payments Standard, or both set up using PayPal Payments Pro. If you have one set up for Pro and the other set up for Standard, the credit card checkout button in your cart would not work properly for some payments.

I.e., if you want to use PayPal Payments Pro for your main PayPal account and also want to use Micropayments, then your PayPal Micropayments account must also be enrolled with PayPal Payments Pro and integrated with E-junkie as a PayPal Payments Pro account. Conversely, if your Micropayments account has to be a PayPal Payments Standard account, then you could only use PayPal Payments Standard with your main PayPal account as well, so in this case you'd need to select PayPal Payments Standard in your E-junkie Payment Preferences. To offer a card-based checkout option in the latter scenario, you may wish to consider integrating E-junkie with 2Checkout or Authorize.Net.