Please hlep with backing up computer with 2 hard drives using true image 2009

hi guys hope you can help. here's the scenario. i have a toshiba laptop running windows vista home premium. this laptop has 2 hard drives i.e. C:\ and E:\. i did a full backup after a fresh install with administrator account active with the latest updates and various software i love using. the issue is, one day my computer crashed for some unknown reason. i used acronis to restore that image. everything restored perfectly but was amazed that my E:\ had disappeared. funny enough when i reinstalled using my vista recovery disk E:\ reappeared. The million dollar question is, am i backing up or restoring the wrong way. how can i backup and restore without losing my E:\ ? thanks in advance