Should I charge my clients a setup fee or only a monthly fee?

Neither is better than the other. It depends on how much work you must do up front. If the setup is a lot of work and the client knows it, for example rebuilding their website, charge a setup fee.

A setup fee is also a closing tool. You can say the normal price is the monthly fee plus the setup fee, but if they sign up on the spot you will waive or discount the setup fee. That gives you an extra lever to close a deal without cutting your monthly price.

In the SaaS Configurator you enter a setup fee on a plan's pricing option. A plan can have several pricing options, for example one with a setup fee and one without, and you choose the option you want when you collect payment.