If all you want to do is add ĉ, ĝ, ĥ, ĵ, ŝ, and ŭ (and the capital versions) to your keyboard in the third (and fourth) positions, i.e., altgr+c=ĉ, shift+altgr+c=Ĉ, you can edit a file in /usr/share/X11/xkb/symbols. You want to edit the file for the country whose keyboard you use, so for me it would be /usr/share/X11/xkb/symbols/us. (You will have to edit the file using sudo.)
You can assign up to four characters per key (normal, 1 ; shift, ! ; altgr, ¡ ; shift+altgr, ¹).
So for example, in the us file you would change
key <AB03> { [ c, C ] }
to
key <AB03> { [ c, C, ccircumflex, Ccircumflex ] }
The syntax remains the same: jcircumflex Jcircumflex, etc. And the accent on ŭ is a breve accent, so change that one to ubreve and Ubreve.
When you are done you will have to cd /var/lib/xkb/ and sudo rm *.xkm and then reboot or just log out and back in.
There is likely a more simple way to do what you want, but I know this way works, since it's a part of how I made my own (ridiculously) modified keyboard layout.