When you are in FSSC (i have 1.5.8) you save your work for editing as *.scn or *.apt. Finish your work on, then (After saving!) go file > export scenery wizard. If you have FS2k2 installed to the default location then your 'Base Location' should be C:\Program Files\Microsoft Games\FS2002\Scenery\[sceneryname] . If it isn''t then check your file paths in options.
Then if you go to the Base path in explorer or whatever then you will see *.bgl files in the scenery and *.bmp (Or posssibly *.r8 in old scenery). It is that folder that you highlight in your Scenery library.
Dan


P..s Sorry forgot your last question:- Set it to either 0 (for the water runway) or your airfield's height.