As an agency, is there a way to allow our customers access to only to own/private pods, and only charge our agency?

Yes. Go to Billing, and create a Private Business Pods. All membership for these pods is billed directly to you (instead of your customer). Your customers will still need to add the Lempod extension into their browser.  Give them your pod's secret code so that they can join it. They will not need to enter any billing information.