Erm, do you know how to build a website? Have you got a functioning website up yet?
Also, regarding how to "transform the value into hex", most programming languages (including whatever language your site uses) should have simple to hex and to dec operations, though if you're modifying a value, it isn't necessary to transform a value to hex,
because hex and decimal is basically just different ways to represent the same value.
All you gotta do is to write the value as byte (or however it is expressed in the programming language you're using)
Congratulations, I see you understood what the documented data on bulbapedia mean.
What is this "SEC00" you speak of?
As in you don't understand how they're stored, or don't understand how to find it in the save?
If it's how they're stored (if I'm not mistaken):
Think of the hex 0xFF, in binary it's: 11111111
Now look at 0xFE: 11111110
and 0xFD: 11111101
Each 1 or 0 represents whether a Pokémon is seen/caught (depending you're at seen or caught offset).
For each byte->binary, the furthest right is the smallest value, starting from 0, and ascends up for everything Pokémon seen/caught.