Each franchise, working within a WAR (Wins Above Replacement, per bb-ref) budget, selected historical players to seed their franchise. This group was augmented by a somewhat arbitrary top-40 NeL players, and a handful of 19th century players and/or players who “belonged” to franchises not represented in the league.
The budget led to some difficult choices–as an example, the New York Gothams (the New York and San Francisco Giants franchise) start in the WBL without Barry Bonds, instead opting for the duo of Christy Mathewson and Willie Mays as their franchise anchors (in addition to Al Spalding, Bill Terry, Buster Posey, Pop Lloyd, Carl Hubbell, and Carlos Moran).
Each of these players enter the league towards the start of their careers, and received a 5 year contract.
Each team additionally maintained “franchise rights” to a handful of players. Many of these players were in the 3,000+ players comprising the initial draft class for the WBL; the rest will appear on the franchise when, randomly, they appear in a rookie class down the road
Sticking with the Gothams, this meant the franchise starts with Gaylord Perry, Juan Marichal, Will Clark, and Willie McCovey as well, with each of them signed for 3 years. These players entered the league at points throughout their career, but almost always with at least a few peak season remaining.
It also means that, whenever they enter the WBL, Homestead will hold the rights to Bonds, Mel Ott, Roger Connor, and Tim Keefe.
You can see on each team’s home page the Seed Players, the Franchise Rights players, and the players for which they hold Future Rights.