For 1., You are writing an purchase invoice over £6 pounds with the name of your bank (if you want you can create an supplier with the name of your bank beforehand). Then you tag the amount in your current account, or wherever you hold the charged amount, with the invoice just created.
2.: You should create an merchant account in the “Banking” section where you create an purchase (credit) entry for the Gocardless fee, which you tag to an purchase invoice for Cogardless (like the same you did for the £6 before). You also create an sales invoice (money in) for the money you received from your customer in the same way. For more info read here Setting up your bank accounts and Handling payments from merchant accounts
3: It is actually the same. In your banking section should be already a Petty Cash account. The money you get you have to write an money in entry and tag it to the sales invoice which you have to create for that sale. If you transfer money to your bank account or one of your other accounts you just tag it as a transfer between your accounts. If you pay rent or whatever you create a money out entry and tag it to the invoice for that purchases. So, if you get £250 cash that is a sales entry in your petty cash account. When you then pay £200 to your bank account is it a £200 credit entry in your petty cash account and a £200 money in entry in your bank account. And your petty cash account has still £50 (which you can spend for whatever you want as long as you create a money out entry in your Petty Cash account.
I hope this helps, if not you can find a lot of info in Welcome to the Knowledge Base
Please note, I’m not an accountant and I don’t work for quickfile