Generally we say 'ベッドで寝る’。If you want to emphasis on 'bed', then you can say 'ベッドに寝る’。 For example, when you go to the hospital, a nurse says ’ベッドに寝てください’。 ’ベッドに寝る’ doesn't short sentence of ’ベッドに入って寝る’.But normaly we think it means ' ベッドに入って寝る’。I hope you can understand it！

会議は　3時に終わります（The meeting will end at 3 o'clock） 会議は　3時で終わります ( The meeting will end within 3 hours) で　 describe a stitch of time に point in time 教室で　本を　読みます(dynamic state usedで) 図書館には　いろいろな分野の　本がある（static state usedに ） if you know this ,it will be easy to find out the different between ni and de ~

It's all here: http://www.guidetojapanese.org/learn/grammar/verbparticles