It's all automatic now and I have not found a good reason to go back to manual.

However it is a good idea to know about GPARTED. It's even usable on VM partitions as we read http://www.techrepublic.com/article/how-to-resize-a-virtual-red-hat-enterprise-linux-partition/

The unknown megabyte could be partition alignment (more at https://www.google.com/search?q=linux+partition+alignment but again, automatic does this for me and with disk space cheap as borsch I don't fret if 5MB is lost here on a 1TB HDD.)

The only people I know this bothers are the ones the run LFS Linux. More at https://www.google.com/search?q=linux+from+scratch

By now you get a partial idea of my view on this. I want to spend time using my PC, less time tinkering.