An Alignment Type is a label that can be applied to the relationship between a territory and a team member, an account product, or a geography. While this is an optional feature, it can be very useful in situations in which the same person, product, account, or geography is aligned with different territories for different situations.
The Alignment Types workspace enables you to create new alignment types, based on your business needs, that can be used with all territory programs. The alignment type is used to automatically align objects with root or branch territories. Alignment types are optional and customized to each organization, so no alignment types are available out of the box. The most common alignment types seen are primary types and secondary types. For example, within the same territory, a specialist who provides a unique service can be assigned as a secondary sales representative and compensated at a different rate.
Alternative example: Let’s say that Bikes in Motion has a single territory that has two assigned positions: a sales representative and a product specialist. The sales representative is the primary alignment, while the product specialist is the secondary alignment. When we align each position to the territory, we can designate different alignment types to differentiate the role that each position plays.

Administrators can create and specify alignment types that can be used when aligning an account, product, or geography with a territory. The Allow Managers to change the Alignment Type option on the Detail tab of a territory program indicates whether a manager can change the alignment type for a particular territory.