While installing be sure to select manual partitioning.Linux will not automatically find ur partitions U wants to keepjust see the partitions and understand the partition which you emptied/backuped.select that and make a /boot partition of ~98-100MB and remaining use as "/" root partition.Ubuntu installer is console based and use SPACE,TAB,ARROWS,ENTER to navigate and select.if u press in while in boot prompt F1 to F8 keys,U will see a lot of options which U can USE if You know Your Hardware.
if u r not sure of ur emptied partition while looking from Linux,just boot with live cd and open a CLI(command Line Interrupt) and use "fdisk -l" to see Ur partition schema.also livecd may have mounted ur partitions in the desktop itself(like Knoppix).browse for empty One.Use it for install.
Code:
suryan:~# fdisk -l
Disk /dev/sda: 80.0 GB, 80026361856 bytes
255 heads, 63 sectors/track, 9729 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Device Boot Start End Blocks Id System
/dev/sda1 * 1 625 5020281 7 HPFS/NTFS
/dev/sda2 626 5989 43086330 f W95 Ext'd (LBA)
/dev/sda5 626 1221 4787338+ b W95 FAT32
/dev/sda6 1222 1532 2498076 b W95 FAT32
/dev/sda7 1533 1666 1076323+ 82 Linux swap / Solaris
/dev/sda8 3004 4567 12562798+ b W95 FAT32
/dev/sda9 4568 5357 6345643+ 83 Linux
/dev/sda10 1667 1678 96358+ 83 Linux
/dev/sda11 * 1679 3003 10643031 83 Linux
/dev/sda12 5358 5989 5076508+ 83 Linux
Best fo LUX.