The problem is that you probably don't understand enough to not be confused (and confused you are).
The big bang comes first, matter comes later. To be only "vaguely" familiar with quarks and leptons does not help. You need to know the details of WHEN things came to be. And HOW they came to be at that time and not another. And it is damn complicated! No question about that.
But these are technical details... let's go back to the basics.
Physics describes what we see. The world is here. This means that at some point the energy we see today was here.
If YOU want to believe religiously in energy conservation (which physicists don't, they keep testing it experimentally all the time, which the undereducated public simply does not know about), the logically correct conclusion is that something must have been there before the big bang (well, actually ... since there might have been no time before the big bang, that expression does not cover the most likely scenarios).
Now, as long as you don't demand a discrete event that started it all, there is no contradiction with physics which does not claim that the big bang is "the beginning". It only says that the big bang is probably an event horizon before which we can not probe much of anything of what happened. That does not mean that nothing happened. We might just never get to know about it. Tough luck.
Neither is it there much of a contradiction with proper philosophy which can't say ANYTHING logical about this because it does not have a non-arbitrary and non-religious starting point.
Now, of course, if you don't believe religiously in energy conservation, which is the proper thing to do BEFORE one has made sure with observations and experiments (e.g. at LHC) that it holds even during the early and even "before" the big bang, a whole new set of scientific opportunities open up. But at this point we don't need any of them. We can live fine without such speculation until we find an EXPERIMENTAL fact which requires us to think otherwise. At which point WE will. Energy non-conservation would allow to construct a discrete beginning and a finite universe and everything else, by the way. And if it turns out that we can EXPERIMENTALLY show that energy/matter appears out of the nowhere at some very high energy threshold in elementary particle interactions, we might just be done. Science can not rule this out without building accelerators or other experiments which get us all the way to the scale of quantum gravity.
The smaller and smaller subatomic particles we speak of are simple the ones we see in our experiments. We did not order the dish, we are just trying to find out how the cook, nature prepared it. You need to work on your understanding of what science is. And what it isn't. The starting spark is, at best, your Christian-Judeo upbringing speaking (or just medieval Western philosophy). It for sure ain't science terminology.
Physics does not search for the origin of the world. It searches for a complete understanding of it. Therefor it cares nothing about "creation" questions. Which might very well imply that we have to forgo getting an answer to "why" it happened. Science does not answer why questions. Only religion does. But if I may remark, it does so poorly and it usually requires you to throw out all the "how" answers. I think religion needs to work a bit harder on that one...
:-)
As for dimensionality: you need to learn to distinguish between fact, theory and hypothesis. ALL dimensionality questions in cosmology, particle physics, general relativity etc. are purely hypothetical. We do not have a single experimental fact about them. Which also means that we do not have a single theory about them. Here is how it goes:
Fact -> hypothesis -> experiments/observation -> theory.
All we have right now are hundreds of hypothesis and not a single fact to prove them. That's why we are building LHC, the new gravitational lensing facilities, next generation Microwave Background Experiments, precision torsion balances to probe gravity at short distances etc..
The decades to come will probably be the most amazing in all of science. I am looking forward to them!
:-)