Starting a project + running into hurdles

For some reason i just can't seem to grasp the whole formatting the correct settings and starting a project
We've been taught to name our conventions, put things in files etc. At the start of most projects i seem to stumble accross what sounds like simple problems but to me are huge hurdles that i can't seem to get my head round. I'd like to think over the course of this second year i have attempted to improve on my organisation skills as not only does it help my concentration but i also get pleasure out of having my room, my life and my work flow organised. I now try to make lists and reminders of priorities i need to sort out in my every day life as when i'm not organised i struggle to get anything done.

It takes me so long to start a project and tuck into a software because i don't always no where to start most the time. So after two days of tucking into after effects i get that feel good factor of creating something i had no idea how to do a couple days before. I question myself why didn't I start this two weeks ago, i could then start to picture what my short would look like, and then BANG! 1 file is mission, and my background of clouds now look like the multicoloured teletext page on an old school tv. Clearly this is something to do with where i have put my files but after hours of playing with after effects i don't understand why it's come up.

I parent-constraint the eyes to the eye joint, but when i move the eye controller the head mesh moves. I got rid of any influence in the head and eye but it doesn't change anything.

A similar occurrence happened when i tried moving the head up and down. Again i was having difficulties with the influence.

When binding the skin to the alien it attached all good and well. I was able to move the limbs but when i smooth previewed both the mesh the clothes dispatched from the mesh. 

With all this in mind and not too long before i need to have this complete, my simplest approach is to avoid weight painting and animating. I will render out single frames of the alien in different positions and place it as a 3D layer in after effects so it will look as if the aliens are there.