During checkout, if your payment methods aren't showing up, go into Admin> Modules> Payment and check:
1. Is the payment module Installed? If not, click the Install button on the right-hand infobox.
2. Is it enabled? Some payment modules allow you to turn them on or off by clicking the Edit button and setting the status to true/false, on/off, etc.
3. Do you have any Zones associated with this payment module? If so, then likely by removing the Zone configuration from the payment module will allow you to use it during checkout.
To properly configure zones with payment modules requires that you create zones to fully match the zones to your customers' addresses. Always be sure to have at least one payment method WITHOUT any zones added to it, or else there will be customers who cannot go through checkout ... and then you'll lose a sale!