scripting workflow

I just have a few questions regarding workflow when producing scripts. First off, do people prefer to have all their code in one file? Or multiple separate files? I know functions and classes are good to keep in separate files, but i am talking about say for example a news system, etc. Next off, how about when actually assembling the files? Do you produce all of your html output, then say build all of your functions - then say build the logic? Does that make sense? I had in the past use DW for building php apps, and as an exercise to myself I am forcing myself to hand code to learn better. But I do however want to increase my productivity. If anyone has any pointers on this type of stuff - it would be much appreciated! Thanks! d