From time to time we're all guilty of rushing through a site design and development phase and using poor organization and bad file naming habits. The more you work on professional sites the better you'll get at it but that's no excuse. Someone else may be working on your site in the future and you may not be around to hold their hand and explain what's what.
When these things are all over the place you'll find yourself eating tons of project time just hunting for those necessary files. This costs the client money and will make your workdays much more difficult than they should be. Just because you're short on time is no excuse to not place the proper files in the proper places. You'll be happy you did in the long run.
So, in closing - get and stay organized! Future generations of web designers will thank you and you won't come across looking like an amateur, you'll look like a professional.