Disclaimer: Base set up really depends on the player and there isn't a 'one right' way. Your teammates might tell you different. I have explained what I was taught and anyone is free to correct me.

Last Island

Your "last" island is the long island before the home section. As you level up, the lay out and towers will change.

Genreal

No matter what level you are, you should group the farms and lumber mills in the back of the island with either a storm (later will be replaced with a crystal howizer) in the middle.

Levels Under 44

If you are under level 65, you haven't unlocked all flaks yet, so your base is going to look different.

The back area will remain the same, farms/lumber mills in the back with a storm in the middle.

In front of that, you would want to put a BLUE MAGE and cannon tower(canon will be replaced later).

Like usual, RED MAGES, should go in the middle of an island slot. This position helps shield all surrounding towers from red spells.

Since people under levels 35 haven't unlocked all the towers, the front of the island will vary between towers. Usually, there is a storm and one defense tower.

Levels 65 and Above

By now, you will have unlocked all defense towers. This is the stage where you will begin to replace cannon, archer, trebuchet, etc. with stronger towers such as flaks and turrets.

The back of the island will remain the same, except that you will place the crystal howitzer in the middle.

In front of that there will be the BLUE MAGE and a STORM TOWER.

Like usual the RED MAGE will be in the middle, as it's the ideal spot for the red shield .

The front of the island can vary. Some people put both ice and fire turrets, while others do a mix of a flak and turret.

Shrine Island

Levels Under 45

At this stage in the game, you will have hopefully cleared out the Shrine Island. This is the second island on your base which houses the SHRINE DRAGON. This island can vary, but as you grow you will be using stronger towers.

Levels 65 And Above

Shrine island set ups can vary, but I personally use most flaks on that island. In the back I would recommend putting an Earth flak or and an Ice flak.

In the middle, there is another red mage, as they are critical to blocking spells.

In the front there should be a Fire flak and a Dark Flak. Dark Flaks are best in front as their ranges are shorter than most flak towers and they deal heavy damage.

Kill Island

The next longest island is referred to as the Kill Island. This island will consist of your strongest towers. Usually, people who are 400 or higher start to build a kill island.