Thankfully, it's not much of an issue for my ship as it will be for yours, since my largest facing section is bow/aft. I wouldn't worry about not having enough thrust power just yet. The goal is only to get this beast moving, anything above that is bonus when she's fully done. You don't want to slap on a shittone of engines only to have to rip them out because you don't have enough power to run them all.
But I do have some suggestions for you. If you've used up the entire aft plate section for engines and you still don't have enough, don't shy away from extending some pods out from centre hull and building some thrust units there. Aside from spreading your critical points out instead of one big blob aft, it also gives a pretty cool look when you fly by someone.
Having said that though, two big 'engines' is better than four small ones. The less design entanglements (Like I did on SH's 4x4 block units), the better. If you can afford the space (Like I can) Then go for it, all the extra armour around the engine units the better.
And as a last resort; if in doubt, cheat. Build some 'impulse' engines (Engine units inside a hull pod), or double stack your engines (one after the other with a one block gap in between rows) inside the engine housing.