Here is a comprehensive list(hope I didn't leave anyone out!) of properties on the beach with two bedroom cottages or suites. As it is comprehensive(I hope...), I did not exclude properties with upstairs units. The list runs from south to north....
Shields has a two bedroom unit:
http://www.shieldsnegril.net/rooms.html
Have you looked at Beach House Villas?
http://negril-hotels.com/accommodati...ean-suite.html
This is one of my favorite spots. Very well run by a long-time staff. Great food. Quirky and cool.
http://www.whistlingbird.com/
Very cool place this is...you wont be beachfront, but the walk is...oh...less than a minute:
http://www.hatihatijamaica.com/rates.html
Another place with two bedroom units....worst part of seven mile beach for beach, though...
http://www.mariposahideaway.com/rooms.html
Interesting place, great tiny bar:
http://www.gatehousevilla.com/rooms.html
LazyDayz......not sure of the current status of the beach...
http://www.lazydayznegril.com/bhouse.html
http://www.nirvananegril.com/cottages.html
Here's one, ground level at a fantastic hotel:
http://www.cocolapalm.com/photos/cocoSuiteE/index.asp
BeachComberClub......personally....I don't think its worth it unless you get a great dealio..very high
http://www.beachcomberclub.com/rooms.htm
Crystal Waters
http://www.crystalwaters.net/rates.htm
Negril TreeHouse...very well run hotel
http://negril-treehouse.com/welcome.html
SeaSplash
http://www.seasplash.com/room-views.html
Our Past Time.....last stop on seven mile beach!
http://www.ourpasttimenegril.com/Apartment_1.shtml
All of these properties have two bedroom units, almost all with a kitchenette...
Happy Researching!