You didn't give us very much information. However, if you have an aftertaste that is a flaw, it's better to fix what is causing the aftertaste. In addition, using honey to bottle instead of something else, won't get rid of an aftertaste.
I don't know who gave you the advice of using honey for bottling to get rid of an aftertaste, but it isn't sound advice.
We'd like to help you, but need more information. The information that we would need are:
What is your recipe?
What is your brewing process? extract? all grain? partial mash? steeping grains with extract?
What is the aftertaste?
If the aftertaste is cidery, are you using a lot of table sugar? If you're using a lot of table sugar, in place of Malt Extracts, you'll get a cidery (unpleasant) flavor. Using honey at bottling will not get rid of that.
We're here to help, but you have to help us understand what's going on, so that we will know how to fix it.