As far as I go, never trust automatic partitioning options in Ubuntu installers, as you may end up with nasty surprises. When installing Ubuntu, personally I always prepare the partitions manually. Since you want to keep a dual-boot set-up, most flexible would be to create a new extended partition and inside it create the several logical partitions.
In the extended partition I usually I reserve:
- 5GB for
swap (or whatever appropriate given your RAM)
- 25GB for
/ which will contain all your system files (but some will say that this is overly generous, as 15-20GB could suffice given your installation habits)
- the rest for
/home which will contain all your user data
I tend to use ext3 file system for the above partitions for reliability reasons (but you could of course use ext4 or reiserfs if you so prefer). Sometimes I include a /boot partition no bigger than 500MB using ext2, but I cannot remember if this is more hassle than necessary; from memory, this is where kernels and grub config files end up.
Additionally, see My approach for replacing current Ubuntu with newer for a discussion on how manual partitioning can be approached.