Setting up Waypoints using coordinates for Prefabs

I'm trying to set up a waypoint system for my prefabs to follow once they spawn since you can't place the physical location for the waypoint game objects without them being the already present. I'm using a vector3 as a varible coding the location in. The problem is how to get them to move to that location without suddenly teleporting to it.

Any suggestions on how to move them between two waypoints, loop the movement a few times and then move to a third waypoint?

By the sound of it all you want is to use Vector3.Lerp. Have a look in the docs for that.

Basically after your prefab is spawned use Vector3.Lerp to move it from its spawnpoint to the first waypoint. Then pause for a few frames if you want, then Lerp to the next waypoint.

Lerp = linear interpolate

transform.position = Vector3.Lerp(startPoint, endPoint, factor);

startPoint = where the object will be if factor = 0.0

endpoint = where the object will be if factor = 1.0