Which Juniper switch and version of Junos are you running?
Typically a WAP will connect to an EX port set to trunk mode.
The native VLAN id will generally be the management network for the WAP
Each SSID then generally has a VLAN tag assigned
You will create these three VLANs on the switch and assign them to the trunk port. The exact commands will vary depending on the model and version of Junos.
To keep the VLANs separate I would assume you have the default gateway for the VLANs on a firewall which can then control traffic between them.