Having the deck just between the engines could end up in a major mess in more than one way... Two quick recipes for disaster are having for mothership to use engines in combat, or a damaged figter's pilot losing it and docking into an engine :)

It’s more of Emergency Hanger Deck. The main decks are located on the front arms. This one is kind of like the lunch tubes in Battlestar Galactica, if you have ever seen them. Kind of like a gun that shoot the fighter out of the ship. Then they will return threw the main hanger areas. I am thankful for your concern and welcome any more ideas that you have that could help in ship design.

Hm. The idea I usually work with is "start from inside" :) In this case... If it's just an emergency launch tube, how do the logistics of that work out? I.e., how are the fighters transported. Having separate launch and dock decks is a good idea, but you need to have to set up the whole infrastructure inside for moving them around, repairing, outfitting, and quick. As well as emergency infrastructure, too -- to take care of damaged crafts, especially unstable, and to switch to different decks essentially in an instant if one gets disabled for whatever reason.

I mostly did design for more realistic physics world (i.e., not the "aircrafts in space" AKA "engines give you speed, not acceleration" physics) which had a major need for way more engines on any craft (at least both forward and aft, as well as rotational), and had way more focus on kinetic weapons than direct energy.

Another world was fantasy space, i.e., "waterships in space" kinda like SpellJammer or Treasure Planet, so I don't think those designs would translate into your world too well :)