For beginners, using the root word of the verb is really good enough.
Besides, the prefixes are not often used in the spoken form, even among the Malays.
It is mostly used in newspaper reports and official documents.
For all beginners! I suggest to start focus on prefixes & affixes only after you reach per-intermediate level.
It will be easier to learn and understand once you have enough vocabularies and understand sentences structures.
So don't worry unnecessarily about something that is not that important.