There are road & river connections to Tarapoto, & buses from there to the Pacific coast.
If you want to take a trip to Pacaya-Samiria National Reserve, you're better off going to Lagunas by yourself and booking a trip from there. The only thing the tour agency in Yurimaguas will do for you is buying a ticket for a boat (only one way) and booking a tour in another agency based in Lagunas.
You can visit restaurant "Mil Sabores" near to plaza de armas church
There are a few hostals in the main town (around the Plaza da Armas). However, most boats allow you to stay overnight before the start of the journey, and for no extra charge.
Visit yacuruna - jungle amazon adventure (Plaza de armas downstairs) and ask Winston for all boats to Iquitos schedules. You can stay the night in his hostal.