For further reading, you should study the chapter A Pragmatic Philosophy/Software Entropy from The Pragmatic Programmer by Andrew Hunt & David Thomas. It deals exactly with your problem here. I will drop this quote from the book:
One broken window, left unrepaired for any substantial length of time,
instills in the inhabitants of the building a sense of abandonment—a
sense that the powers that be don't care about the building. So
another window gets broken. People start littering. Graffiti appears.
Serious structural damage begins. In a relatively short space of time,
the building becomes damaged beyond the owner's desire to fix it, and
the sense of abandonment becomes reality.
Don't leave "broken windows" (bad designs, wrong decisions, or poor
code) unrepaired. Fix each one as soon as it is discovered. If there
is insufficient time to fix it properly, then board it up. Perhaps you
can comment out the offending code, or display a "Not Implemented"
message, or substitute dummy data instead. Take some action to prevent
further damage and to show that you're on top of the situation.
Are you going to throw away all of the prototype's code? If not, and you're going to build upon it, then don't make your life harder by leaving broken things pile up. You may find comfort in thinking that you'll repair things later, but this also makes you oblivious to the piling, and you might just overlook serious and otherwise obvious flaws.
Tip 1: After you're done writing a method, read it again, start-to-end, and see if it cannot be refactored.
Tip 2: When you're not actually writing code, and have the time, take a few minutes to look over your code and see what can cause trouble and what can't. If you can afford it, fix everything on the spot. If not, then at least set a TODO there, and write down what can go wrong and why, so you remember the next time you're visiting the code. I call these 'quick refactoring sessions', and I perform them quite often.
I find that the most important ingredient in refactoring early and properly is willpower. Be sure to have some ready!
My third tip is extracted from the book itself.
Don't Live with Broken Windows