wporg is the version uploaded to the official wordpress plugin repository, it's a slimmed down version that removes the auto-installer for licensing reasons. You want the main (non-wporg) version.

If you have a woocommerce installation you want to use BareBits with, you can either install barebits separately or just install the wordpress plugin and have it install BareBits alongside itself automatically. I would suggest the automatic method.

The benefit of a separate installation would be the ability to have multiple woocommerce stores connecting to the same BareBits installation if you wanted to do that for some reason.

Fees are automatically taken out of incoming payments. The "fee due" gradually accumulates. Once an incoming payment is less than the fee due (for example, say you owe 1000 sats in fees and the incoming payment is 500 sats), that entire payment will be redirected to pay for the fee. This is all shown transparently in the BareBits dashboard and invoice list so you can keep an eye on it. Basically, instead of your customer paying you for that checkout flow, they pay us. We do it in this way to keep the software fully self-custodial.

If you have a cashu mint enabled, fees can also be withdrawn from the cashu mint via lightning once they reach a certain threshold. The cashu mint (if enabled) is the only funds your installation of the BareBits software actually has access to, since all other incoming payments go directly to your off-server wallet via NWC, CLINK, LNURL, Strike API, or on-chain address. Funds in the cashu mint are also automatically swept to your off-server wallets as often as possible to reduce cashu-based risk.