You have full control over which clients see or do not see the option to use Joist Payments.
You can turn the payments options on or off on each invoice you create or edit.
You can also set whether the default behaviour for Joist Payments is to be turned on or off for all new invoices. You can do this from the Settings > My Account section in Joist.
Even with the default option set to off, you can always enable payments on a given invoice if you like by turning on the payments switch in that invoice.