According to the Apache manual http://httpd.apache.org/docs/current/mod/mod_headers.html#header you should use append
:
Header append Set-Cookie "poodle=noodle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT"
Header append Set-Cookie "tweedle=puddle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT"
or according to HTTP use comma to separate multiple values:
Header append Set-Cookie "poodle=noodle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT, tweedle=puddle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT"
or use Header add
if you want avoid comma separated cookies in one header to follow suggestions in RFC 6265 section 3 (as noted by @SteveC):
Header add Set-Cookie "poodle=noodle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT"
Header add Set-Cookie "tweedle=puddle;path=/;Secure;HttpOnly;Expires=Wed, Jan 01 2020 2:02:02 GMT"