Edit your ~/.Xresources file and add a ...*Font: (sommething)...-iso8859-2 resource for each program you want to use with them. Use xfontsel to choose the right font/
add a setxkbmap -layout "en,sk" -option "grp:alt_shift_toggle" command to your .xinitrc and .xsession for sk-us keyboard, with alt-shift toggling enabled.

and of course, consult xkb documentation, found somewhere in /usr/X11R6/lib/X11/xkb or somewhere

Btw this is not a NetBSD issue, but rather a XFree86 one

fine.