You can toggle between showing the actual time, and the time on this particular puzzle, by tapping on it.
If you want to hide the clock completely (some people prefer to play untimed!) then you can choose to do that from the Settings screen (the cog icon from the title screen.)
You can choose whether each letter you enter is duplicated throughout the grid (this is on by default) or you can turn it off if you like to enter it manually (some people like the sense of completion!)
For the entries in the grid that are there when the puzzle starts, just tap on each of those letters in the cipher area to fill those into the grid.
During the game you can ask for a hint at any time;
The first time you tap for a hint, it will display a count of how many entries in your cipher area are incorrect.
If your tap it immediately for a second time, it will also highlight (in an orangey shade) the letters which are incorrect, so you'll know which to change!
The game will watch out for any letters which you accidentally use twice - we call those collisions. If you do enter a letter in the cipher for a second time, it will highlight in purple the letter and the one it's colliding with, so you can look to see which of them to fix!