"Win7 creates a 100 MB partition that I don't want." You don't have a say in it, it's a reserved system partition that Windows 7 will make.
If you use the custom install option you can specify how big a partition you want for the W7 instalation and either create a second one or leave the rest as unallocated space to install Ubuntu on.
I would disconnect the second drive when installing W7, otherwise you may finish up with some W7 system files on one drive and the os on the other. This will be a pain in the a*** if you need to remove the drive at a later time, when you think that it's not a system drive.