I think c8kdreemz did bake the cookies with the sticks in. If I understood the problem correctly, the sticks were coming out of the cookies when she was either decorating them or placing them in the bouquet.
If I want the sticks baked in the cookies, I follow a tip I found here on CC. You bake a short stick in the cookie, then take it out to decorate. Use royal icing to keep them in after they are decorated. It helps in two ways. You can bake more cookies on a sheet with the short stick. The stick is not in the way when you decorate. Sorry, I do not remember who the OP was for that thread.
The other method I use is Shiney's stick on the bag method. This way you do not bake the sticks in the cookies, but hot glue and tape it on the bag. Then you just put the cookie in the bag and tie with ribbon.
Here is a bouquet I did with the first method.