New to SSD's, files automatically saving to them.

I know there is a lot of guides out there on subjects such as this but I am having a bit of a difficult time doing what I need to do and have already kind of dug myself into a hole here.

So firstly, windows isn't allowing me to delete some files due to permission issues (Folder would belong to system and when I try to change ownership to myself or anything involving that I get permission errors and nothing I have read has worked.)

Ontop of that I have a M4 Crucial 128GB SSD which I want to use as my boot disk as well as for a few games and all my drivers just for quicker loading times etc etc, in conjunction with the 128GB SSD I have a 1 TB Seagate HDD that I want to use for the more mass amount of my storage such as documents, music, movies, general games etc etc. I have already installed things such as AVG, Chrome, Skype, Vent, and 2 of my more majorly played games on my computer and everything I download is default saving to my SSD when I'd rather it save to my HDD and move it to my SSD after. I know theres a bunch of guides out there on how to setup your HDD as your primary drive for all your files and what not but going through the guides most don't account for people like me who had installed programs already without setting up these paths (Like I said im new to ssds and didn't think about this before hand).

Can anyone lend me a hand to get me out of this so that I get everything setup the right way?