Why is it important to raise/lower both ends of the bike together?
There are two things that change when you change the height of one end of the bike or the other:
Whenever you make a change which has the side effect of changing the ride height, you should try to make a change to counteract it and get things back where they were.
Making the fork angle steeper (closer to vertical) makes the bike steer more quickly. This can make the bike feel twitchy and unstable if you take it too far.
Unfortunately, ride height is a relative thing, so setup is difficult to translate from bike to bike, and will be affected by things such as:
When in doubt, stick with the stock settings. If you think you need to change the steering geometry, make small changes, take careful notes, and measure everything before you start, in case you want to change it back. Don't ride aggressively until you are fully used to the different handling you now have.