I grew up mainly a console gamer and always dreamed of playing things like Wing Commander. The games are at a great price so I got 3 and 4 and a logitech extreme 3d stick. I'm having trouble getting a feel for the flying. I'm not sure if I am supposed to be "leading" my shots at the enemy ships or waiting for them to straighten out and take my shots.

I really want to get into the classic flight games like these, SW TIe Fighter and any others you guys can recommend.

Once you target an enemy, press "L" to lock, a green aiming reticle should appear.
I hope this makes it easier for you.

Other games in the genre you should definately get are Freespace 1+2 and Independence War 1+2.

You have to lead them, in the first two games only some fighters have a lead indicator when you lock on the target to you will have to guess (it becomes quite natural after a while).
However locking on the targets is vital anyway since you will be able to follow them on the radar nad allows missiles with a guidance system to lock onto them.
You should also read the manuals if you haven't already, there are a lot of lore bits and some gameplay advice in there.
Since you have a Logitech stick, I advice you to dowload their software off their webstie to map the additional buttons.