There actually is an apparo (ad + paro). The prefix ad- was assimilated and the 'd' turned into a 'p'. The word apparo means to prepare or provide.
As C.M. Weimer commented, in- has an accusative sense which means to or into. There are many compound verbs prefixed by in which carry this sense, such as ingredior, infero, and ineo.
There is another explanation for the meaning of impero. Compound verbs often take a dative, and the meaning of this dative is often related to the prefix. Considero impero tibi, which means "I give a command to you". See how the preposition "to" in the English translation conveys the sense of the prefix? Another example would be absum tibi, "I am absent from you".
So, considering the accusative sense of in-, the meaning of impero is quite logical.