lanie
Why not apply for planning and see what happens. Planning process likely to take 6 months +. Could be much longer - deciding on house layout, drawings, application, further information, Bord Pleanala etc.
If you take the glass half full approach ( scarce these days ) to the economy perhaps you will no longer be in negative equity by the time you are ready to sell / build.
Word of warning for when the build is imminent. Most punters including yours truly drastically underestimate the cost of building and finishing their own home. Lots of people will telly you to get a budget and then add 25% fro changes / contingencies. I would say a figure of between 25% and 50% is more realistic. Builders tend to offer quotes for the bare minimum and disguise this fact cleverly. So you will find yourself adding extras, changing for better spec etc. All money!
Good luck