Unfortunately the pet store employees are not trained on all the different species their store may carry. They extrapolate the basics of reptile care they are familiar with (and that depends entirely on who you talk to), and chameleons often break the mold with their more unique requirements. So while the pet store employees often have good intentions, remember that they are there to make a sale, they are not experts and often have no experience with chameleons at all. It is also in the store's best interest to promote the purchase of more stuff...which may or may not be (usually is not) the stuff you need.
The good thing is now you've discovered a treasure trove of correct information here on the forums! We will help you get set up correctly.

You've already done a good job to separate them quickly. We are in this for your chameleon's best interest and health so don't think we are just picking on you or anything. Pet stores make people have to start over all the time.
The best thing to do would be to fill this out based on your big cage setup, so that we can help you fix the other mistakes they've told you:
Chameleon Info:
Your Chameleon - The species, sex, and age of your chameleon. How long has it been in your care?
Handling - How often do you handle your chameleon?
Feeding - What are you feeding your cham? What amount? What is the schedule? How are you gut-loading your feeders?
Supplements - What brand and type of calcium and vitamin products are you dusting your feeders with and what is the schedule?
Watering - What kind of watering technique do you use? How often and how long to you mist? Do you see your chameleon drinking?
Fecal Description - Briefly note colors and consistency from recent droppings. Has this chameleon ever been tested for parasites?
History - Any previous information about your cham that might be useful to others when trying to help you.
Cage Info:
Cage Type - Describe your cage (Glass, Screen, Combo?) What are the dimensions?
Lighting - What brand, model, and types of lighting are you using? What is your daily lighting schedule?
Temperature - What temp range have you created (cage floor to basking spot)? Lowest overnight temp? How do you measure these temps?
Humidity - What are your humidity levels? How are you creating and maintaining these levels? What do you use to measure humidity?
Plants - Are you using live plants? If so, what kind?
Placement - Where is your cage located? Is it near any fans, air vents, or high traffic areas? At what height is the top of the cage relative to your room floor?
Location - Where are you geographically located?
Pictures are helpful