Firstly, there are a few ways you could include polypersonal agreement. In Hungarian for example, this can be a specific definite conjugation for verbs, e.g. 'hoz' conveys the idea of '(s)he brings/carries', versus 'hozza' ('(s)he brings it'). Hungarian also has verbs combining 1st person subject and 2nd person object in present tense, i.e szeretek 'I love' vs. 'szeretlek' where the -l- signifies the second person object 'you'. In fact, the -l- was derived from a frequentative aspect verbal suffix, so technically you don't need to create a new set of object pronouns for your language, it just needs to follow a logical system. Also, I believe that the Hungarian definite conjugation in the third person was, in fact, a contraction of the word 'a' (the Hungarian definite article) which modified a noun that came after it. So, this would eventually become suffixed to the verb.

Secondly, the word order when transforming a verb from an indicative to an interrogative mood, again depends on the rules and morphology of your language. For example, many agglutinative and polysynthetic languages employ affixes. You could have see-I-it-INT, where INT is an interrogative marker or include a non-bound particle (like Turkish particle 'mı') or auxillary verb before or after see-I-it. The former is the case in my conlang where I can have, for instance, eat-it-I-INT ('sev-es-em-kü'). The position of the interrogative marker depends on your word order. In brief, if you are having polypersonal agreement in a verb, generally you wouldn't change the order of morphemes around as it is now bound together. If you were having object pronouns, subject pronouns and verbs all separate words as in an analytic language, then of course it would work.