How did Walter and William Bell know to start preparing children for a "war" before Walter initiated the Zero Event in 1985?
tl;dr: They didn't know about the war until after 1985, because Bell is the one who created the war in the first place. Before that, they were just doing an unconventional drug trial.
Because most of this is told in flashbacks, the timeline is a but fuzzy, but Bell and Bishop were not preparing the children for "war" prior to the Zero Event. They originally started doing clinical trials of Cortexpihan as a normal medical drug. It was designed to help slow or stop the natural deterioration of the brain as we aged, so the trials were done on children. However, they noticed that some of the children in their trials started having strange side-effects, such as telepathy.
Several years later, while the Cortexiphan trials were still going on in secret (they were officially ended in 1983 but kept going much longer), Walter discovered the secret to crossing between universes. However, he realized right away that his method damaged the barrier, so he was afraid to use it again, even to put other-Peter back. Instead, he hoped the Cortexiphan would produce a child capable of crossing over safely, and sending Peter back that way. Although he did manage to bring that ability out in Olivia, it was uncontrollable, and Peter began accepting his new reality as home, so Walter abandoned that idea.
By this point, though William Bell had his own ideas. While studying existence the other universes, and the effects of Cortexiphan on people like Olivia, Walter had figured that it would be possible to destroy both universes, and use the resulting energy to kick off a new, controlled Big Bang. That would allow him to control everything about the new universe, effectively becoming God. (This, by the way, is the thing that terrified Walter so much he had his brain cut out).
While Walter quickly rejected this idea, Bell didn't. Instead, he formulated his own master plan. He decided to intentionally start a war between the two universes. He wrote the ZFT manifesto (on the typewriter Walter would later acquire from him -- with the wonky "y"), which described the collision of the two universes and that only would survive, knowing that it would drive any ZFT adherents to prepare to fight the other side. He also began using the Cortexiphan trials to bring out talents suited for soldiers.
However, Bell's premise that only one universe could survive a merge was fundamentally not true. He just wanted to encourage both sides to start a war, because he wanted both universes to be destroyed. He wanted to use the energy of the two universes, and the power of the Cortexiphan kids, to help him create a brand new universe, with himself as God.