Setup primary/secondary keyboards in X, e.g.:
XFree86Config-4:
Option      "XkbLayout"     "czsk(us_cz_qwertz)"

Keyboard shortcuts setting:
pressing e.g. Alt + F1: 
* primary keyboard (english): yields A-F1
* secondary keyboard (czech): yields Button6-F1

However, xev reports  for left Alt key in BOTH keyboards keysym Alt_L:

KeyRelease event, serial 27, synthetic NO, window 0x1c00001,
    root 0x40, subw 0x0, time 4800836, (-680,352), root:(416,374),
    state 0x2010, keycode 64 (keysym 0xffe9, Alt_L), same_screen YES,
    XLookupString gives 0 bytes:  ""

As a result of the inconsistency, it is not possible to use the same keyboard
shortcuts in both keyboards.