Making HDD Primary After Windows 7 Install?

(Long story below, feel free to scroll to the bottom paragraph just to see what the problems are I am trying to fix).I've been trying to get help on this issue all day and I am at the point in being lost that I am close to just finding out how to wipe the drives clean entirely and not use my SSD for my boot drive. So heres my issue.Yesterday I built a new computer. It has a M4 Crucial 128GB SSD and accompanying it is a Seagate 1TB HDD. My plan was to make my SSD the boot drive (which was easy enough) and then use the HDD for mass amounts of storage and just put a few of my most used programs/applications on the SSD to improve the speed of them. Well turns out that it wasn't that easy because I didn't think before hand to make changes or anything and all of the things I have been downloading/putting on the new PC have been saving on the SSD, a few things that were selectable for installation I manually put into the HDD (another problem with that coming up.Essentially when trying to delete a few files from the HDD I didn't need, I was told I wasn't able to due to not being the owner of the file (the folder is owned by SYSTEM) and all of the google-able solutions I tried didn't work such as changing permissions and setting my user account as owner.So essentially I am REALLY hoping, for the sake of my sanity and frustration level with building a new pc () that you guys can help me figure out why it won't delete these folders (nothing in the folders themselves are being used) and help me setup my HDD to be my primary drive where files/programs/folders save and being able to transfer files from my SSD over to my HDD. I am new to the whole SSD thing and already am regretting it despite how amazing its performance is.Edit: Also just to give you a bit more information, I am using a Windows 7 Home Premium 64Bit disk (OEM) to install windows.