Leveling up I would like to make sure all or most skill trees are leveling up at a simliar pace, to be versitile without having to go back and grind too much at endgame. I realize the weapons will be the trickiest.

Using Dragonknight as an example, when I am doing quests, or playing solo in PvE, it's best to always keep 1 of each skill on bar so you level everything evenly? Also making sure atleast 1 type of each armour equipped as well. So far Dragonknight for example, you would want to keep 1 Arcanic, 1 Draconic, 1 Earthern, then lets say Soul Magic, and Sword and Shield. Then equipping like 5 Heavy, 1 Medium, 1 Light. So that should make all those skill lines level up somewhat equally?

Then moving on to next question would be how do I ensure Fighter's Guild, Mages Guild, Undaunted level up as I progress as well?

The guild skill lines level off actions you do in the world, not using their skills. So you only need to equip a skill from those lines to rank up the skill itself.

Fighters guild for example increases rank for killing undead and deadra. Mage guild for finding lore books, and Undaunted for completing instanced dungeons. The individual skills within those categories can rank up from being equipped but the skill line itself levels up from the above.

Also armor levels based on how many pieces you have equiped so going 5H 1L 1M will not level them evenly. In that example your heavy will out level your light and medium.

just the play the game. the skills you like to use will level up. the skills you don't use, you won't use. so why even worry about them?