Morgan's TWD Timeline:
Season 1: Morgan & his Son are the first non-Walkers that Rick meets after he wakes up in the hospital. Rick separates from Morgan & his Son to find Lori and Carl, but not before Rick gives Morgan a radio and a promise to communicate at sun-up everyday. Rick attempts this a few times, with no success.
Season 3: Rick and Michonne happen across crazy "clear-mode" Morgan while out looking for food & supplies.
Season 5 (finale): Daryl brings Morgan back to Alexandria (if you recall Morgan found the map that Abe wrote "The World is gonna need Rick Grimes" on, to which he shows to Daryl and that is why Daryl takes him back to Alexandria) , right as Deanna tells Rick to shoot the Pete (aka: PD) for killing Reg with Michonne's katana. A shocked Morgan says "Rick??"
*It was between seasons 3 & 5 that Morgan met up with Eastman and made cheese and became "Zen Morgan". The episode (Here's not here) was a flashback.
Fear the Walking Dead is currently sitting in between seasons two and three of the Walking Dead's timeline. That is how Morgan will fit in. It's in between he & Rick separating in season one and meeting again in season 3.