I uninstalled Ubuntu via "How-to-Geek" instructions, but upon completion my boot menu is gone and I can only boot the simple "grub" command line. Booting to my Live USB with Ubuntu works though (I am using now) but when I go to reinstall I no longer have the option to make a new partition to dual boot windows too. I must somehow make a new manual partition if I want to be able to dual boot to windows.
A little more detail: I just figured out that I can still load my old windows desktop if I directly select to boot from it from the Bios menu, so I know everything still works fine. So the issue is just that Ubuntu is not seeing my windows partition and is only giving me the option of writing over the whole thing.
You're going to want to select the "Manual" method if none of the automatic methods are working as you expect. It really isn't that scary, so don't worry.
All that you're going to need to do is correctly identify the partition(s) that your previous Ubuntu installation was using, and tell the installer to use those.
The "If you have disk that contains Windows installed" answer to this question should in particular be of use to you, except you do not need to follow step 4, since you already have the space freed.
How to use manual partitioning during installation?