I actually did this for myself a few months ago. The process is a bit long, and read through the entire thing before you make any decisions as to whether you want to do it or not. You will need to change your registry, and although I have not experienced any problems so far, you may if you don't do everything as I did.
First, set up your partitions in a Ubuntu live disk. Copy all your information to a safe volume in case something happens. Then, wipe all your drives.
Install Windows first. When you create your account during installation, choose a spare account name. It doesn't matter what this name is, except for the fact that it cannot be the name you want to use in the future. I would call it something like "spare."
After installing Windows, create an account with your real account name, but do not log into it yet. Go into regedit, and change all instances of C:/Users to D:/Users (or whatever drive you have your storage on, be it D:, E:, F:, G:, etc. Don't change anything like C:/Users/Administrator, though, only the ones with C:/Users and the ones that would pertain to you.
After doing this load of registry edits, go and restart your computer and log into your new account. If you've done everything right, your new account's profile should be in the drive you had set it to be.
If it is, great. Delete the spare whose account is still on C:/. Do whatever you want on Windows, and after that, install Ubuntu.
I can expect that you can install Ubuntu without any instruction. During installation, I installed my user folder in the normal directory in the same partition as my main installation. I then created symlinks on my user folders by using the commands:
rm -r ./Documents
ln -s /media/Storage/Users/Tyler/Documents ./Documents
rm -r ./Downloads
ln -s /media/Storage/Users/Tyler/Downloads ./Downloads
rm -r ./Music
ln -s /media/Storage/Users/Tyler/Music ./Music
rm -r ./Pictures
ln -s /media/Storage/Users/Tyler/Pictures ./Pictures
rm -r ./Videos
ln -s /media/Storage/Users/Tyler/Videos ./Videos
Tyler is my username on Windows, and Storage is the name of my storage partition.
These commands don't include the templates and the Desktop folder, although I expect that they would be easy to implement.
These symlinks do not have the pretty images, and I have not found a permanent fix for that at this moment. I can set the icon image, but it is reset. I suspect that this is because it needs to mount every time I start up, and that resets the images. I'll post a fix if I find one.
If you want to automount your storage partition upon startup in Ubuntu, you'll need find which partition to mount. In a terminal, use
sudo fdisk -l
You should receive a list of partitions. Mine looks like this.
tyler@Tyler-PC:/$ sudo fdisk -l
[sudo] password for tyler:
Disk /dev/sda: 320.1 GB, 320072933376 bytes
255 heads, 63 sectors/track, 38913 cylinders, total 625142448 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0xf64a0fce
Device Boot Start End Blocks Id System
/dev/sda1 * 2048 125831167 62914560 7 HPFS/NTFS/exFAT
/dev/sda2 125831168 188745727 31457280 83 Linux
/dev/sda3 188745728 608364543 209809408 7 HPFS/NTFS/exFAT
/dev/sda4 608364544 625141759 8388608 82 Linux swap / Solaris
Search "Startup Applications" and add the command
udisks --mount /dev/sda3
sda3 should be replaced with the one for the disk you have. I had remembered that I had set mine to sda3 when I made my partitions. Also, it is my largest.
After that command, upon startup, you shouldn't need to navigate to your storage partition via nautilus to mount it. I'd only discovered that fix yesterday; as I use Eclipse to develop in Java, needing to mount it via nautilus every time was extremely obnoxious.