No matter what area of programming we are talking about, the rule of thumb is to create small manageable pieces that are well organized and well labeled. Whether this is pieces of data in a database, or the directory tree for your website files. Sometimes this takes extra effort because you need to think of the best organization scheme and then know how to properly link the files to each other so that the program still functions, but in the long run it is well worth it, your code will become much more reusable, readable and debuggable.
The best way to approach a new problem is to think how it should be done, and then regardless of how difficult that might feel, because this could involve learning new techniques, you should do it that way. The alternative is to look at a problem and immediately fall back on what you already know because that will seem easier and faster but in this way you won’t learn anything new and down the road the project that you have created will be less manageable or possibly hit a wall when it stops even being functional and has to be re-written because it wasn’t done properly the first time.