If you do not want Shorewall to destroy your nice tc orders generated through htb.init, you need to make some shorewall configurations. After Shorewall 1.3.13 you just need to edit /etc/shorewall/shorewall.conf and set:

TC_ENABLED=Yes
CLEAR_TC=No

Prior to this release, you need to restart htb.init every time after modifying shorewall (there is an option in the admin menus of shorewall just for this).