The easiest and probably cheapest way for 2 people with bags to get to Entrecampos train station from Lisbon airport is by taxi!
Bus may be cheaper but will require changes and it may be a hassle with bags.
There are two trains departing Entrecampos on Sunday evenings that meet your needs:
Dept: Lisbon Entrecampos: 17:30 Arr: Faro 21:10
Dept: Lisbon Entrecampos: 18:51 Arr: Faro 21:55