Two SkyDrive folders on laptop Win 8.1

HELP!!

I have two SkyDrive folders on my Win 8.1 laptop (Sony Vaio Pro 13") and it is causing some serious file management problems. One folder is linked to my SkyDrive favorite shortcut in Windows Explorer, but it is not linked to the internet SkyDrive, causing files to not properly sync. The other folder syncs with the SD, but I have no ability to make things available offline or online-only. In an effort to correct this on my own, I managed to wipe my online and connected device (laptop, desktop, Surface) SkyDrive folders completely (ARGH!!), and am in the very slow, very tedious process of restoring from the SkyDrive recycle bin on the website. This is now causing conflicts as I restore, creating many folders with (1) at the end (duplicates), but they are empty.

So, currently I'm stuck with not being able to mark things as online-only on my limited capacity laptop SSD (I have a 256GB SSD and 44GB of SkyDrive storage), as well as somehow duplicating many files on my SD and eating up a bunch of space in my account. Please help!