Morgan served as Ginsberg's personal archivist and bibliographer from the early-'80s until the author's death of cancer in 1997. Over their 20-year professional relationship, Morgan became quite close to Ginsberg, and has written extensively on the Beat Generation and its key figures.

Bill Morgan's interest in the Beats goes back to the early 1970s, when he was attending school at the University of Pittsburgh. For his master's degree thesis, he compiled a bibliography of the works of Lawrence Ferlinghetti, poet and owner of City Lights Books, the famous San Francisco bookstore and one of the most important publishers of the early Beat writers, most notably Allen Ginsberg. After finishing his thesis, Morgan was encouraged by the editors at the University of Pittsburgh Press to pursue this project with a view toward eventual publication. He did indeed continue his research, working in close collaboration with Ferlinghetti as his personal bibliographer, and, after a decade of research, he published Lawrence Ferlinghetti: A Comprehensive Bibliography (New York: Garland Publishing, 1982).

By 1980 Morgan had moved to New York City. While he was still working on the Ferlinghetti book, the San Francisco poet had referred him to Allen Ginsberg, whose own personal library and archive were invaluable sources of information on the Beats. Early consultations with the poet grew into an enduring relationship that lasted from the early 1980s until Ginsberg's death in 1997. During these years Morgan served as Ginsberg's archivist and bibliographer, helping the poet to organize and maintain his ever-increasing library and records. As Ginsberg's bibliographer, Morgan spent fifteen years corresponding with and visiting numerous publishers, editors, scholars, and library collections in order to gather sufficient information to document the history of Ginsberg's prodigious output and the worldwide attention it has drawn. The results of his research appeared in a two-volume bibliography: The Works of Allen Ginsberg, 1941-1994: A Descriptive Bibliography and The Response to Allen Ginsberg, 1926-1994: A Bibliography of Secondary Sources] (Westport, Conn.: Greenwood Press, 1995, 1997). In 2006, Morgan published I Celebrate Myself: The Somewhat Private Life of Allen Ginsberg(New York: Viking, 2006). He followed that in 2010 with The Typewriter Is Holy: The Complete, Uncensored History of the Beat Generation(New York, NY: Free Press, 2010).Morgan has also authored or edited a half-dozen other works relating to the Beats, including collections of Ginsberg's essays (Deliberate Prose: Selected Essays, 1952—1995, New York: HarperCollins, 2000), of the poet's last poems (Death & Fame: Poems, 1993-1997; coedited with Bob Rosenthal and Peter Hale, New York: HarperFlamingo, 1999), and of Gregory Corso's correspondence (An Accidental Autobiography: The Selected Letters of Gregory Corso, New York: New Directions, 2003). Through City Lights in San Francisco, he has published two guides, A Walking Tour of Jack Kerouac's City (1997) and A Literary Tour (2003). The latter appeared during the fiftieth anniversary celebration of City Lights, to which Morgan also contributed with a series of free walking tours of the North Beach section of San Francisco, once a center of bohemian life in the city and a past home for many of the Beats in the 1950s and 1960s.

In the course of his decades of research on the Beats, Morgan gathered perhaps the largest private collections of printed works by and about Ferlinghetti and Ginsberg in private hands. Recently, finding it increasingly difficult to maintain these two very large and valuable collections in his New York City apartment, he reluctantly determined to part with them. Knowing that Ferlinghetti was a UNC-Chapel Hill alumnus, he decided in the fall of 2001 to offer his collection of the San Francisco poet to the UNC libraries. Discussions with library officials led to the transfer of the collection to Chapel Hill in December of that year, partly as sale and partly as gift. Pleased with the outcome, Morgan then offered a similar arrangement for his even more extensive Allen Ginsberg collection. The materials were delivered to the Rare Book Collection in Wilson Library in August 2002.