Here are the two most important rules for tuning:
A hole will give a higher note if it is placed closer to the mouthhole. It will give a lower note if placed farther away.
A hole will give a higher note if made larger. It will give a lower note if smaller.
These rules mean you can “raise” a note by enlarging the hole or by placing the hole closer to the mouthhole. You can “lower” the note by using a smaller hole or by placing the hole farther from the mouthhole.
It also means you can change the hole size and its placement without changing the note. A larger hole could be placed farther from the mouthhole, or a smaller hole placed closer to the mouthhole.