Tokida you protect me/he/she/it
Tokita he/she/it protects me/you/him/her/it
So, how can you clearly mark the object or patient in this sentences? Well, Kareyku relies in these cases in context. But even when context is not clear enough you can always use the independent pronouns to mark it. In those cases where you mark the pronoun, the subject will always be understood to be the subject of the transition.
Shin tokida you protect him (you are protecting him)
Odan tokita he protects you (he's protecting you)
Pretty simple. To this, of course many additions can be made. For example the use of prepositions or even evidentials.
ikani odan tokitas.
1st-ADD 2nd protect-4T-EV
He is protecting you with me
I thought this was worth mentioning. Needless to say, the object or patient of the transition can be either omitted or expressed. In those cases where the patient is a pronoun to over express it will have an emphatic sense, otherwise it's just correct.
tokikal ikanu lani
protect-2T-EV 1st-GEN heart
I am known for protecting my heart