How long was Lilith been under the NERV HQ and did it say when was she
 captured?

Well, they never give any specific data on this (they tend to avoid doing
that; Hideaki Anno is one obscurifying man) but there are things you can tell
by inference.

The Geofront was not discovered until post-Second Impact. So that means either
Lilith was moved there after Terminal Dogma was built (which means you can't
put her in there until 2002 at the earliest, those buildings take TIME to
construct, and Gehirn didn't have the kind of resources Nerv does) or they
found her in there in the first place, which means you can basically have her
there from the Begginning of Time onward if you so desire. A specific capture
date is never given, so you can basically go nuts.

A point, however; I've heard speculation that the Lance of Longinius was being
used to inhibit Lilith's growth by being impaled into her. This may be an
important fact, depending on what sort of story you're writng, but I can't
really confirm it because I don't know for sure. It's just something you
should be aware of.

-Mercutio
"A plague 'a both your houses!"

"We've secretly replaced Ikari Shinji's
LCL with Folger's Crystals. Let's watch
to see if he notices the difference....."
-Akun Daniels, "Anime Death Match."