So Substitute takes away 25% of of the users HP. But how is the HP loss calculated if the Pokemon's HP isn't equally dividable by 4? Since you can only take evenly dividable amounts of HP, will it be rounded down or rounded up? For example, if a Swampert have 406 HP and it uses Substitute, will it lose 101 HP or 102 HP (since 406 divided by 4 is 101.5)?

Everything is rounded down in Pokemon. So 101.