Hi there VorteX_,
Do you have two partitions of the same HDD or two different HDDs?
In case you have two partitions of the same HDD, you can go to Disk Management, delete your E: partition and extend your C: partition. Keep in mind that you need to back up the data that is on E: before you delete the partition.
In case these are two separate drives, you can just free up some space on C: and start storing your data on D:. You need to do this manually as it will not happen automatically.
Here's how you can free up some space on your C: partition: http://www.howtogeek.com/125923/7-ways-to-free-up-hard-disk-space-on-windows/
Hope this will help,
D_Know_WD