Eyeliner is probably the most feminizing thing you can do to your eyes, partially because it's such a subtle darkening around the lashes. I suggest you try and figure this out. I don't remember ever having a problem with my eyes twitching while I was applying it, but I've been doing it since I was 10 or so. This might help...
Exercise your eyelids: hold them shut tight, open them wide, repeat a few times. More exercised muscles are less twitchy. Looking in different directions while you do this might help, but looking ahead seems to get the most muscles.
Stretch your eyelids: use your fingers to gently massage and pull around them, getting that whole area less tense. That might be what's making then quick to twitch.
Desensitize your eyelids: hold the eyeliner gently against the skin of your eyelid, wait for it to stay still, then start gently moving it around until it stops twitching again.
To apply: Look down, gently rub the end of the pencil above your eyelashes, then (if you have the dexterity) lightly rub it against the underside of where they come out. Look up, start under the eyelashes, and do the same thing. It's possible just learning to apply well and practicing will help you with the twitching.