Keep training your abs. It is unlikely that they will develop enough to cause your stomach to protrude. I would suggest that as your BF% decreases so will your waist size. If your BF% has been elevated for some time you will probably lose a lot of internal BF as well as subcutaneous BF thus making you waist much smaller as you lean out.
Good luck, keep training the abs hard, and be patient. If you eat clean and continue adding lean body mass without excessive BF accumulation over time the cicumferance of your waist will decrease.