Okay, Let's all agree that "You can lead a horse to water but, you can't make him take the bird out of the bush." "Ziva David"
What you are wanting to do is against the practices of 99.999 percent of the Zen Cart community. You are the ONLY person I have ever known who would beat a horse to death rather than feed it.
That said, here's some info that may be of help. It's going to be somewhat generic as you have yet to answer any of the posting tip questions that tell us information we need to know.
I hesitate to do this and will add a disclaimer right here that I would NEVER do this on a customer's site. IMHO, any warning is vital to ensuring the customer's site is functioning correctly and should be first on the priority list after any upgrade, change, modification, deletion, addition, etc. But, we just like to check our work before moving on.
As an IT professional, I'm sure you know how to use search but, it's pretty obvious that you are new to Zen Cart so... Here's some info that may help and educate you on one of the really nice features of Zen Cart.
In your_admin directory (Which I hope you have renamed something other than admin), there's a drop-down menu with the heading of Tools. Under that menu item is the selection Developers Tool Kit.
When the Developers Tool Kit is open, the last option is Look-up in all files.
When Zen Cart sends out something like Warning:, Notice:, etc. it does so with variables that are set in a define statement. Generally the Warning:, Notice:, etc. is hard-coded into the PHP while the actual message is what is contained in the define statement as a variable. In this case, you would enter "Your database appears" (without the quotes) into the Key or Name: field of the form.
Under All Files Look-ups:, select All Files - Catalog since the burr under your blanket is the cart.
File Type and Case Sensitive can be left alone.
Click on the search button.
If there are two files that are shown, you have at least had the forethought to create a custom template. If only one appears, you have created another can of worms in a future upgrade, but that's fodder for another thread when you start having those problems.
If there are two files, then you would open the file that is associated with your_template. If only one, you would open that file (and maybe look at custom templates later?).
Again, as an IT professional, I'm sure you're aware that the file should not be opened in Dreamweaver, Word, FrontPage, or any other editor that adds proprietary code to the resulting file. NotePad is good but, if you can afford it, UltraEdit is great.
Also, as an IT professional, you know that a define in PHP can sometimes be made to "go away" simply by properly removing the define from the define statement.
Once all this is done, you MAY have the warning disappear. I'm not going to setup an incorrectly upgraded test site to see if it works.
IF it doesn't work, then you well know (as all IT professionals do) that you can add a display:none to the stylesheet to prevent the entire warning from ever showing up.
Being an IT Professional, I'm sure you have Firefox with the Firebug add-on or something similar for viewing the stylesheet on line.
Again, these are two methods that I DO NOT RECOMMEND BE USED by anyone, IT professional or not to remove any warning. They ARE excellent ways to find and adjust items in Zen Cart that are not known to all IT Professionals.
PS
I would like a survey of all IT professionals who have "task lists to follow" that have ever really been able to follow them. And, more importantly, who (other than you) would not abandon any task list to ensure that the product is functioning correctly.
PPS
You need to step back a bit and realize that some of us old timers (in more ways than one) are only trying to steer you in the right direction. Most of us have tried the "I know this, so I don't have to try to learn the way this is done in Zen Cart." You've found yourself in a foreign country and want every bartender to speak English. When you get in the mindset of "asking for a beer" (programming) you need to learn the "local language". Best of Luck with your new language.