If you have another partition with lots of free space it would be a good place for your folders.
Having both in C: will cause a lot of fragmentation. Filling up C: is not good for Windows either.

Also, make sure you set up your paging file to be separate from both the downloads and
Windows Partitions and set it's minimum and maximum sizes to the same value to lock it
down. I tend to create a simple FAT16 partition of about 4 gigs with nothing but the paging file
and very little free space left over. This will speed up paging and prevent it from leaving a
mess of fragments on your OS and work disks.