If a Scout troop is chartered by a religious organization, the head of that organization, or someone he recommends will become the chaplain. In a case where the troop has no religious affiliation, a local member of the clergy can be approached to perform this role.
Note, that most Pastors, Rabbis, etc. are very busy, with a number of demands on their schedule. While the BSA documents assume they will have plenty of time for this role, that's not always going to be the case. In many cases, there will be one or more older people in the congregation with the spiritual background who may be able to fill this role, with the Pastor's endorsement.
Because most troops have multiple faiths represented, this can be far trickier than picking out someone to work with a youth organization that is wholly made up of church members.
This person must be able to work with boys from various faith backgrounds, and encourage each boy to grow in their religious faith... even if the chaplain himself follows a different one.
The chaplain would certainly be able to invite families to join the church at weekly worship service, but should not proselytize, or push his faith upon families or youth within the unit. This person should be accessible to the youth and their families, sensitive to their needs and be willing to help them.