OK, call me "Old Fashioned", but I recommend after the install to verify that you can now boot into BOTH the Ubuntu Linux AND MS Windows systems. After the Ubuntu installation process, from now on when you boot up your computer, you will be presented with a menu with two options: Boot Windows or boot Ubuntu Linux. You should test that these two selections work properly. I must still be paranoid from all the Linux installs that I have done over the years....

... on the other hand, I have yet to encounter an install problem when using WUBI (except for students not having enough hard drive space on their Windows partition)...