What is the best way to configure a DAW using multiple drives?

Currently, I am using a modified HP Pavilion m9300t CTO. Intel Core 2 Quad CPU Q6700 @ 2.66GHz 2.67GHz 8.00 GB RAM
64-bit OS, x64-based processor. Running Windows 10 Pro 64-bit and SONAR Platinum.
My C: Drive is a SanDisk X400 128GB SSD SATA III 6GB (contains OS and SONAR) 
     E: Drive is Samsung HD161HJ 160GB 7200RPM 8MB Cache SATA III (contains Page File)
     J: Drive is WD My Book 1230 3TB USB External Hard Drive (*Free, but I intended to use it for "Libraries" etc.)
When I first configured in this way, the Boot time was 23-24 seconds. But as time goes on, it takes much longer (at times almost a full minute). And initially, it seemed 128GB would be plenty, but the OS footprint has continued to creep up to the disk limit due to Windows Defender and Cumulative Updates. I now have 111GB used and 7.22GB free. I am thinking I would have been better off to use C: for OS only, and SONAR on E: (not sure now if the external drive J: should be used at all).
Money can be an issue for me. I'm on a very tight budget.

And also windows update files.
 
I would suggest upgrading the 160GB HDD to 500GB or 1TB and loading most of your applications on it.  You can get a WD Black 1TB drive for $75 from newegg.
 
Alternatively you could upgrade your SSD to 256GB and you should have plenty of room for Sonar and the OS.

My laptop has 3 internal drives but a common USB3 external drive for projects wouldn't be a bad idea especially if you have 2 different systems running Sonar.