Instead of using one fleet, create multiple fleets that only contain certain types of ships. This give you more control, and as mentioned earlier, is likely to encourage better "walls".
It depends on your strategy, but I'd recommend grouping heavy cruisers with disable/repair support cruisers (Hoskikos, Subjugators, or Subverters). This helps heal the ships suffering the most damage and allows the disable abilities to be put to use.
I'd stick your larger support cruisers (Cielos, Guardians, or Overseers) with the long-range frigates and anti-strikecraft ships. Ant-strikecraft ships are very effective against fighters, which are the bane of long-rang frigates. Though bombers will be hitting your heavy cruisers, anti-strikecraft ships are the first ships targeted by heavy cruisers under auto-attack, and are far inferior to fighters in taking out bombers anyway, so I'd recommend keeping them out of the front lines. The large support cruisers tend to be better when with the long-range frigates. Cielos help focus firing, which is great for LRMs, and Iconus Guardians keep cruisers away from your Illuminators with the repulsion ability. Can't say much for the Vasari with their Overseer's, you may want those on the front line instead.
Finally, group your carriers together in a third fleet that stays far away from the battle.
Where you put your capital ships is up to you, though I generally don't have them in any fleet. It depends on what faction you play, but most capital ships are better if in the heat of the battle so that they can use their special abilities. I find that fleet formations are much better when no capital ships are in the fleet itself, and get very screwy when you add them. Fleet formations are even worse if you spam one type of capital ship (16 Halcyons will make your fleet super wide).
