Ok bro, the way it works is, after some foreplay, you pull out a condom, say just a sec, open the wrapper and put it on. There is no magical way to throw on a condom (unless I'm seriously in the dark haha).
You just gotta do it, she in all likelihood will not put it on for you, its kinda your job. She will however understand what is going on and one of two things will happen, A) she will assume the position, b) she will say no.
To reduce option b) do the condom maneuver while she is as hot as you can get her. Keep in mind tho she might still say no. Don't feel bad, it happens sometimes. BTW No usually means not yet, but NO always means no
