Manual focusing AF lens?

I'm using a Nikon 50mm 1.8D on the D5000 and I know autofocus will not work because the D5000 does not have a motor. I have to manually focus and I thought it would be easy but I'm having a hard time on it. I adjust the focus ring until I see that the subject is clear but sometimes it's not perfect and I have to try again. When I'm focusing I see a dot light blinking in the viewfinder, what does that mean?

Added (1). Ohh the light tells you when you've focused: D

___
… -'"…''~.,
…,.-"…"-.,
…,/… ",
…,?\,
… /… }
…/… :'^'.}
…/… :"…/
? __… :'…/
… /__.(…"~-,_… :'…/
… /(_. "~,_…"~,_…:'… _/
…{._$;_…"=,_…"-,_… -~-,}, .~"; /…}
…*~_…"=-._…";,./'. /"…/…/
…\'~,…"~.,…'…}…/
…(…'=-,…'…(… ;_,-"
…/.'~,…'-…\. /\
… \'~.*-,…|,./… \,__
,_… }.>-._\…|…'=~-,
… '=~-,_\_… '\,…\
…'=~-,.\,…\
… ',… '\…__
…'=-,…,%'>===''
… _\…_,-%…'\

That's the focus confirmation light, explained in detail in that pesky booklet that came with your camera.

Focus your lens until the light is solid green. That is the confirmation that you are in focus.

Oh my gosh! Manuel is getting pesky already?