Translation:How do you cook?
There's no difference between "Unapika vipi" and "unapikaje", both mean the same. This question is ambigious though, as "vipi" can both mean "how" and "which", i.e.: which foods are you cooking?
and this case it means how like when you want to ask someone how is he. you say vipi hali
I said "How are you cooking" which was accepted, but I was wondering if "How are you cooking it" would also be said the same way, or if you would need to indicate a direct object somehow.
That would probably be said differently with an object infix on the verb. The object infix will depend on which class the object referred to by "it" is from. So it can be "Unakipika vipi?" , "Unavipika vipi" etc. This is just my hunch. You may want to read somewhere else too to verify.