This option is for churches that have separate ministries and receive and track contributions for those ministries in their TouchPoint database. In other words, the donors for both the church and this other ministry are in the same TouchPoint database, as are the contributions.
The Custom Contribution option allows you to separate these into separate statements, one for each ministry with the statements including only funds for that ministry and a Standard Statement for all other funds.
This requires very little setup and we give you the sample code to use as a copy and paste recipe. If this sounds like something your church needs, just take a look at the help article.