If you understand my first alscript help page you should be able to add a second line of secondary structre using the following script as an example.
A second line of secondary structure can be added by running addstruct
twice.
Then you edit the script to tell it where to put the second set of secondary structures.
The main lines in the script that do this are
ss2=`expr $ss + 2` # line of secondary structure
ssl2=`expr $ss + 3` # line of secondary structure labels
and
sed -e s/\$ssl/$ssl/g -e s/\$ss/$ss/g -e s/\$loa/$loa/g $name-c.ss >> temp.als
sed -e s/\$ssl/$ssl2/g -e s/\$ss/$ss2/g -e s/\$loa/$loa/g $name-d.ss >> temp.als
Notice I did have to manually change the name of the .ss file in the sed lines, so its not totally automatic.
The files.