Where to put configuration for xstartup scripts?

[orbitz]

I'd like to do a change such that even if ~/.gnupg exists and ~/.ssh exists, NOT to run gpg-agent with ssh support but instead to use the standard ssh-agent. I can do the code change just fine but what I'm not sure about is where to put configuration information for these startup scripts so a user can specify that they want this behaviour instead of the default.

Should I use environment variables for this kind of thing? Where would those get set?

[digitalist]

cat ~/.xprofile
setxkbmap -layout "us,ru" -option "grp:caps_toggle,grp_led:caps,numpad:microsoft"