Hi,
I have two issues affecting payments for subscriptions:
1. If a user initiates a payment via paypal and it does not complete, I try to go to 'baskets' and click 'pay' to indicate that payment has been made manually. I fill in the appropriate details about how the payment was made and click 'pay'. I then get the error: "Failed to save Pay the basket manually because: This payment basket has no gateway associated so can not be paid manually."
How can I resolve this?

2. Paypal payments are being made, but the web site does not register that they have completed their payment. I have followed the steps as outlined in your paypal plugin: "Go to: My Account: Profile: and in column 'Selling Preferences':
for PDT: Website Payment Preferences: Auto Return for Website Payments: Turn Auto Return to ON and enter homepage of your site, e.g. www.example.com as Return URL (that URL is not very important, you can use same account on multiple websites, as this software sends return URLs with each payment), then turn Payment Data Transfer to ON on same page. Finally leave Encrypted Website Payments off to start easily (you can turn them on later, as this software supports it, see below). Set PayPal Account Optional to ON so that users don't have to register with paypal to pay with credit-cards. Save page and return to page to get your Identity Token to paste in the field below.
For IPN: In My Profile, click Instant Payment Notification Preferences, then Edit. Activate Instant Payment Notification and put your site URL e.g. www.example.com/ as Notification URL (here too, not very important, as this software sends notification URL with each payment). Then Save."

Thanks Kyle,
Ok - question 1 is now resolved
Question 2 - I don't see any notifications arriving in CB Subs - however, the payments are successfully completed in paypal. When I check paypal's IPN notification history screen it lists the IPN's sent with the status 'retrying'.
I have verified that the identity token and the return url (the web site domain name) are all correct.
What to do next?

Thanks for quick feedback.
No there is no firewall on the web site (at the moment anyway). I will install Admin Tools later.
I will pm you screenshots of the settings in paypal - I can't see anything wrong there.