If the nearly full drive is your primary drive - ie has your Windows and other applications on it - and has only 3% or so free it is too full already. Your Windows drive typically needs at least 15% spare capacity for Windows to work efficiently, and this is probably why you are running into lags.
Your best bet is to move blocks of data over to your nearly empty drive. Things like your music files, photos, videos. These all take up big chunks of space and can all be accessed perfectly well from another drive, and the easiest way to move them is 'Drag and drop' in Windows Explorer.
If you have your music in a folder called music in your 'C' drive, just click on the folder and drag it into the other drive. If your music, and I am just using this as an example, is in several different folders then create a folder called 'Music' on your second drive and just drag all these folders into it. And repeat as necessary for photos, videos, etc..
If you want an explanation of how to do this with Windows Explorer, post back.