As far as i know you wont be able to boot directly into linux if you put it on E, because the loader needs to be in the 1st 1024 sectors (been a while since i installed from fresh), however you can use a boot disk (floppy) to load straight in.
Also, be careful selecting the drive, Linux doesnt call it E: but more likely to be HDA1 for C, HDA2... so think it through before you install, if you have 3 drive letters but linux gives you 4 options, choose the last, the 1st is probably the boot loader section...
Also, Linux cannot WRITE to NTFS drives properly, so if you use NT/2000/XP you're likely to have that disk format, just remember if you open up a file on those drives, not to save it there, make yourself a fat32 drive for file crossovers.
Basically, as long as you dont just go full throttle through it, nothing really you can do wrong
and try and use a seperate hard disk if you can, get the hang of it before you go installing on extended partition.