From quick research it looks like some of the comics mention that Wolverine was being manipulated using medication, mind control techniques, and psychic manipulation. The picture below is from Wolverine #68.
The above mentioned website shows comic books and synopses of each one pertaining to his memory implants. It's worth noting that the first one in that site says stuff about them using medication and by looking at the picture it looks like they are using some sort of help with tubes.
Wolverine #129 (Oct 1998) – “Whatever It Takes…”
Writer: Todd Dezago;
Penciler: Leinil Francis Yu; Inker: Edgar Tadeo
Wolverine vaguely remembers his experiences at Experiment X. “Usin’ all sorts o’ medication an’ mind-control, they went lookin’ fer my feral side, strippin’ away every bit of the man I was, leavin’ nothin’ left but the animal inside, primal, savage. While I was in a state o’ constant bloodlust, they studied me, tested me, tried t’find a way t’ control me an’ make me inta their perfect livin’ weapon.”
In another comic we find this :
Wolverine #50 (Jan 1991) – “Dreams of Gore: Phase 3”
Writer: Larry Hama
Penciler: Marc Silvestri; Inker: Dan Green with Hilary Barta and Tom Palmer
Logan discovers a warehouse in Windsor, Ontario, used by Experiment X to alter memories. Specifically, he finds a movie-style set of the location where he, Sabretooth and Mastodon fought the revolutionary who looked like Silver Fox. This would suggest that these events never happened and where created to sow doubt into Logan’s memories. Based on comments by the Professor, it seems that Wolverine, Sabretooth, Silver Fox and Mastodon all had their memories altered at these facilities. The plan was to reinsert the subjects into society without knowledge of their past lives, using a lethal robot named Shiva as a failsafe should the subjects go rogue.
There also seems that there was a psychic involved named Aldo Ferro who helped with Weapon X in implanting Wolverine's false memories:
Wolverine #63 (Nov 1992) – “Bastions of Glory”
Scripter: Larry Hama; Artist: Mark Texeira
Aldo Ferro gives Wolverine a memory jolt so he can remember a time during Experiment X when he used his psi-talents to control Logan in front of the Professor, Cornelius and Hines. Instead of using movie-style sets to create false memories, Ferro proposed using his psychic abilities to more cheaply and effectively alter the memories of the Weapon X subjects. In other words, the Windsor sets that Wolverine comes across were used to create one layer of implanted memories when Logan and Sabretooth first joined the CIA, and a second layer during Experiment X before Aldo Ferro upgraded the program with his psi-talents. Carol Hines argued that it was Aldo Ferro who came up with the idea of tying false memories to pain receptors because he was a sadist who wanted to live forever.
Overall it's clear to say that technology, theatrics, and psychics were used to implant false memories.