Bitfinex - 25% annual funding fee for margin - Fiat vs crypto - how to minimize cost?
What you fund your account with is irrelevant to this question.

If you take a long position against a USD pair, you'll borrow USD and pay USD interest. If you short a Coin you will borrow that coin and pay its interest.

Eg. Open long position on BTC/USD for $1000, you'll be borrowing $1000 for your position and would have to pay back $1000 + Interest.

If you short BTC/USD for 1 BTC, you'll be borrowing 1 BTC for your position and would have to pay back 1 BTC + Interest.