Yes, you can specify which products should appear in your Related Products section by using the custom query string.
In the Factory under CUSTOM VIEWS > Related Products > Product List > click the cog (
If you want to pull products from a single category for example select "Use custom query" under "Product selection" and in the query string field put c=xxxxxx
with xxxxxx the category ID of the products you wish to display. See attached.
Here is a list of other parameters you can use in the query string field: http://www.datafeedr.com/docs/item/154