It's hard to give you any specific advice without knowing a lot more about your level of experience, your understanding of different programming paradigms, best practices, etc.
Having said that I remember feeling like you're feeling on my first one or two software projects (before I had actually considered becoming a programmer). I remember reaching a point in those projects where the complexity had reached a level that my brain sort of "gave up" and I found I couldn't progress on them anymore. I think I was living under that fallacy that I had to understand the whole project at any given time.
Fast forward many years and many shipped products and I certainly don't feel that way. In the broadest sense I think I've learned to embrace ignorance in software development. Developing reusable code is a formalization of that. If you're writing software to be reusable and easy to use (not easy to understand internally) you don't have to have a sense of the big picture, or the whole picture.
If it is the case that you're new to programming, I would suggest limited scope as much as possible. The "simplest" project is always more complicated than you (or I) would imagine. Try creating a very, very small project but take that project to completion.
Alternatively, if you're hitting the complexity wall with what sounds like it could be a fairly straightforward web project, you're probably not leveraging the available tools as much as you should be. If you think that applies pick up a book on RoR or Django, download either of those, and try to build your project (or a simpler version of it) with those tools.
You should also consider picking up a book or two on programming best practices. The problem you're attacking with your software may be unique, but writing big (and small) software projects is a solved problem. There's lots of good advice out there on how to structure a big project, how to write reusable code, how to do basic testing, etc -- all of the techniques people have figured out for making large projects manageable.