Before installing ubuntu, you can setup the partitions exactly how you want them using a livecd like PartedMagic:
and then direct the ubuntu installation to install on your desired partition. PartedMagic is a great tool that you should have in your kit. It has not only gparted, but many other useful utilities.
Finally, you can't format linux partitions from windows without some windows partitioning application like Partition Magic or Acronis Partition Expert. I don't recommend either as the free tools in linux are much better for dealing with linux partitions.