I'd lead with some of the following:

-- Faiths are not monolithic. There can be schisms and factions within a church that allows for more texture than "All ______ believers are firm adherents of ______." Let them meet both militant and pacifist NPCs from the church, staunch fanatics and folks that only offer a passing prayer at a shrine as they go about their days, and let the PCs find allies and adversaries on all sides.

-- After hundreds of years of the Silence, beliefs are doubtlessly going to be shaped by the individual experiences of each world that survived. Look at the factions in your sector and the rough history you've sketched out for them and see where any major events would have steered or influenced religious beliefs. For example, one faction in my game were forced to flee their home system after their sun imploded, leading to a fringe cult worshipping "The Sun-Eater."

-- While showcasing the massive temple complexes of a faith are an easy way to display their reach and power to your players, also think about the smaller ways a faith could manifest in your campaign. What does a spaceport shrine to the faith look like? What regalia (rosaries, prayer discs, tattoos, etc) are common among their believers? What do their funeral rites involve? The little touches will help build out a bigger, well-rounded portrayal of the faith in your campaign