Hi Andy,
Sorry for late reply.
Go to this link, lest you want to take a
shortcut:
Online Payment (cic.gc.ca)
Step by step would be-
(1): Go to
Pay your fees online page and select
Permanent residence and then
No in the bottom-left sections:
Pay your fees online (cic.gc.ca)
(2): Then on
Pay your application fees online page, select
Express Entry under
Permanent Residence. This will lead you to link I mentioned above.
(3): After payment, make sure you get/download/save the
receipt as you will have to upload it under the
Proof of payment section in
Additional documents.
Here are the screenshots:
Express Entry payment
Alongside uploading, I also sent it to them via web-form confirming that I have made the payment, just to be safe.
I hope this helps.

Let me know if it works out for you or if you have any other query.
Regards
Amey