from FAQ
What happens when a monster has a high base attack
bonus, and it uses a manufactured weapon along with a
secondary natural weaponry? For instance, suppose a 5thlevel
lizardfolk fighter wields a battleaxe. What would this
creature’s attack routine be?
Just add the natural secondary attacks to the manufactured
attacks the creature can make. Assuming that the example
character has five fighter levels, she has a base attack bonus of
+6 (+1 for being a lizard folk, +5 for fighter levels). Assuming
the character doesn’t use a shield, she has two natural
secondary attacks available—her bite and her free claw. She
has a –5 penalty when using a natural secondary weapons. So,
when the character uses the full attack action, her attack routine
is +6/+1 melee (battleaxe)/+1 melee (bite)/+1 melee (claw).
However, if the example character were using the standard
attack action instead, she could make only one attack. This
single attack could be a +6 if she used the manufactured
weapon or a claw (a lizard folk’s claws are the primary natural
weapon), or +1 if the character chooses to bite. You always
take the secondary weapon penalty when you use a secondary
natural weapon (see the MM glossary).