Question about FTL

Right now I am using a focus based system on my 2 teams. It becomes difficult if I am in WG and my team happens to get split between 2 raid groups. The focus system breaks at that point and whichever clones are in the other raid group do not follow, assist, etc.

I am looking for a really good write up on setting up a FTL based configuration. I have seen some guides out there that kind of touch on setting it up, but I am still fairly confused about it.

Can someone direct me to a guide that explains it really well?

I hate it when my team is separated in WG.

Before I can point you in an FTL direction what key broadcasting software do you use?

From the tag on your post [Innerspace], I'd recommend taking a look at IS Boxer.
I have a decent write up on my signature.

Also, www.isboxer.com, is worth checking out.
You have a ton of resources in one place.

As far as FTL goes with IS Boxer.
During the configuration, each team member is given a unique FTL modifier combination.
You can go with the default, or change them to your hearts content.

The keys selected here, will only impact three keymaps.
As in, you are free to use the same combination of modifier keys, for other macros or keymaps.
The three Keymaps which use FTL are: FTL Target Me, FTL Follow Me, and FTL Assist Me.
Every other FTL function, calls one of these, and then does whatever.

For example, the FTL DPS keys (1 through =), will:
a) Run.. FTL Assist Me, on the toon who you are on, which has all of the others acquire their target.
b) Press the same key on the slaves screen as the main.

So, all you have to do, is drag whatever spell you'd like straight from the spell book in wow, no macros necessary, onto the keys you desire.
You can place the "Click" macro, for a click sequence here.
You can place macros for healing such as /cast [help] Heal; [help,target=targettarget] Heal.
But the spells right out of the spell book, without any form of assist wow macro, will auto assist the correct toon, just by pressing the hotkey (1, 2, 3, etc).

I use octopus currently and have no clue how to set up the FTL... I have looked for slash commands for it, and am thoroughly confused.

How do I set up the FTL system at all? (sorry if I seem ignorant, I am just not comprehending the FTL system for some reason)

I recently started working with the Jamba macro functions. Basically I made all of my macros like this:

"/assist #master#
/cast #damagespell#".

Then each of my toons has a button, that's not hot keyed. This button does

"/jamba-team set master <toonname> all
/jamba-macro use macros variables all"

So if I need to use another character as the master for whatever reason, all I have to do is change windows and click the "make me master" button. This rebuilds all my macros, and creates my new master as the main assist.

The only problem with this set up is it can't be changed while in combat.
I haven't gotten too deep into it, and the team I started it with is only level 13ish right now. But it seems to work ok for my needs.