Installed goodman 3.5 ton air handler, that replaced old york unit that had fan center relay. a.c. works fine , but how do I wire in the aquastat, so the fan comes on for heat? Is it as simple as putting the 6006 to the fan wire on air handler? Won't that send 24 volts back up the t-stat?

You will probably need a isloation relay between the aquastat and the fan motor relay OR you will have to wire the fan motor with the contact end switch in the zone valve if so equipped.

Post exact model number and pictures of ALL wiring diagrams.