Aux to SIF has a 15 sec cooldown, but if your shields drop you dead either way unless you get your shields back up. Best thing to do is not to let them drop in the first place. Once shields are low everything in STF that has torps will send them to you(expecially the 54k invisible), or you become the easiest target in PVP. Fed ships should focus more on shields and KDF have the comfort of higher hull to work with.
I don't know the resist you get with Aux to SIF but I bet it isn't as good as the Shield heal + the 40% damage resist you get with EPtS 3.
generally I use ASIF as a heal more often, but it is true that if I keep my shields up, I wouldn't need the heal that much. I'll try it out the next chance I get and see how I fare. Tractor beam and my runabouts are mostly there to keep the target in place while I broadside them, that and my horrible turning means I'm going to be missing chances to use tachyon, but still, I'll try it combined with evasive maneuvers and see how my results turn out.
Greetings, I have used a very similar layout since the Atrox has been around. The short: I wasn't impressed...
Basicly, you are a decent supporting healer, nothing more. Most cruisers are simply more viable (Extend Shields, EPtX) in terms of healing. However, for quick things like shield support with TSS/ST as well as HoT from HE, this is more or less decent. The major problems appear once you get focused. You're simply missing the survivability. Once focused, I have to redirect all those abilities just to myself and hit the CD wall pretty soon. It simply got frustrating. The Atrox with such a build sure can pack quite a punch - but only for a very limited time. Adding RSP1 to the Engi mix helps, as well as having EPtS3 in there - but with that, you are losing ASIF2, which is a pretty important quick heal with a short CD. Not only that, but ASIF basicly has no shared CDs, especially not on the Atrox. So you're either off with limiting your own defense or limiting your healing abilities.
The Atrox suffers from an important thing: There is no real place for it. An actual cruiser is better for cruiser tasks like sustained DPS, healing and tanking. A real science ship is more useful in terms of offensive sci abilities. The Atrox howevery mixes both classes somehow together: You'll got all the science goodness - but a turnrate which is even worse than a cruiser. However you're missing all the Engi stuff you'd get from the cruiser.
Most offensive Sci abilities like Gravity Well, Tykens Rift, Charged Particle Burst or Viral Matrix are limited to a 90° firing arc - a bad combination with a slow turning ship. It might not be that bad in PvE, but for PvP purposes, this is more or less useless.
So you are more or less forced to be a supporter, however a cruiser fits this role better. I have yet to find a decent, satisfying build for my Atrox. I've been thinking about using GW3 and more Tractors for trying to become more of a crowd controler, but I don't think this would work out either.
Mongoson: I would say I wanted a balanced build focusing on surviveability and support. I really want to lock down those tactical cubes while my teammates/fighters beat it to death. Unfortunately, whenever that happens I have either too many survival abilities to the point where they don't get used, or too few and the cube rips me apart in moments.
BlindSavior: You are right, I should focus a little less on my own DPS as my fighters are technically doing it for me.
As you say yourself, you have too many support abilities in the setup which doesn't get used.
I've been thinking about using GW3 and more Tractors for trying to become more of a crowd controler, but I don't think this would work out either.
It takes a while to get used to the turning rate of the Carrier, but it's quite adept at filling the Crowd Controller role, as well as dishing out some respectful DPS. 2x Tractors + GW works very well in ESTFs.