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This may seem really "out there", but I keep all the code of a package in one file. Not only does this reduce or eliminate asdf/defsystem maintenance, which I loathe doing, it also helps avoid the kind of habit you described. After all, the edits are all in one place.

To borrow a quote from the movie Highlander - "There can be only one (file)!"

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the first thing I do with any new project is create a directory for it, the package.lisp file and the .asd. That much I do (though I should automate it, like weblocks does with defproject, hmmm)

but after that it's one file, until it gets too bloated and redundant, then i break it to two small redundant pieces.

Thought sometimes its too tempting to do everything in the repl: cramming a fat piece of code into one form and save the result as (setf foo *) if I like what I see :-D usually for experimentation with a new library I'm using for the first time.

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