I agree with Shane. I also am a graduate of the school of hard knocks.
At first your question "How to build a big application with no difficulty?" may sound like a contradiction but it is not. I suggest you contact the closest CLA (Certified LabVIEW Architect, NO I am not a CLA!) in your area and ask them for some assistance. I am not suggesting that you you just contract with them to do the work (although that would qualify as easy). Ask for them to advise on architectures or help with the design devlopement. The issues you mentioned are the normal result of bottom up programming. Its sorta like inventing all of your tools for your workshop before you decide if it is going to be a wood shop or a metal shop. Top down design would start with the big picture/core functionality and then determine what are the challenges and what tools will be required. After that an architecture is assembled that address the requirements and challenges. It is no shame to call on an experienced guide when doing this type of work. You can think of devlopers as explorers charting paths to new technological teritories. And staying with that analogy, even the greatest of explorers in history did not hesitate to utilize the assistace of local guides when avialable. If you can afford a consultant, then I suggest you utilize this exchange to help. Keep your questions brief but to the point. Supply graphic aides when appropriate and we may be able to pull off a "group think" to get you were you need to go. Done rambling for now, Ben