There's no one best build for skill decks, but there are definitely things you can do wrong in building your skill deck. Here we'll discuss a couple general skill deck building strategies and tell you what to avoid doing. Information taken from the Combat for Beginners official TCoS website.
Create a Skill Deck Edit
Mess around with skill placement on a deck with this Skill Deck Builder.
Skill deck building strategies Edit
Keep similar skills in the same column. For example, putting melee attacks in the first slot, melee buffs/debuffs in the second, magic attacks in the third, ranged attacks in the fourth, and heal/escape skills in the fifth. By doing this, you will always know what type of skill is associated with each number. If you need a ranged attack, you know there's one in the fourth slot.
Put a sequence of skills in one column. For example, putting a buff skill in the first tier, a debuff in the second and third, a melee attack in the fourth, an escape skill in the fifth, and a ranged attack in the sixth. This way you can keep using the first column for your attacks, giving you a (more or less) static combat style.
A good way to make sure you can always finish an open combo is to put a combo finisher on a diagonal in your skill deck. This is called a "Hesselian diagonal".
Things to Avoid Edit
Combo openers cannot be used while a combo is open. Do not fill a tier with combo openers.
Pay Attention to Cooldowns
The vast majority of skills have a cooldown associated with it. Make sure you arrange your skills in such a way that you won't be waiting on a cooldown after your skill deck rotates.