Assume DITA source files are stored in C:/sandbox. In the sandbox directory are files myhdr.xml and myftr.xml. The files must be well-formed XML, so myftr.xml might look like this:
<p>DRAFT</p>
In the Ant script that builds the XHTML target, add properties for args.hdr and args.ftr. The target in the Ant script would look like this:
<target name="tk2xhtml">
<ant antfile="${basedir}${file.separator}conductor.xml" target="init">
<property name="args.input" value="doc/toolkit.ditamap"/>
<property name="output.dir" value="out/toolkit/xhtml"/>
<property name="transtype" value="xhtml"/>
<property name="dita.extname" value=".dita"/>
<property name="args.hdr" value="file:/C:/sandbox/myhdr.xml"/>
<property name="args.ftr" value="file:/C:/sandbox/myftr.xml"/>
</ant>
</target>