(The following advice is my personal opinion on patch design for musicians. It does not necessarily reflect my opinion on programming in general, or the views of my sponsers. Use only as directed. Keep out of reach of children. For external use only)
It may seem obvious, but to handle a large project, you must think of it as a combination of many small projects. Seperate the functionality into many small pieces. Learn from the examples provided with Pd and what other people have already done (usually better than you). Then find a way to make the pieces you have work the way you want.
By seperating the pieces (and making use of subpatches and abstractions) and giving them space, your patch will be better organized and easier to modify. You don't have to go nuts and make everything modular "just because you can" if you're not going to use it. You can always add options later. Stick to what you need to make your vision a success.
For big projects. figure out what you are interested in, what you want to accomplish, and why you need to do it a certain way. Then make a plan and stick with it as best you can. Noodling around without an objective is not experimenting, it's just wasting your valuable time. Experimenters form a hypothosis, then test their theory. You music will be better if you have an idea first, and then an implementation. You can do anything you want in Pd so now what will you do?
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