You're dealing with at least five kinds of conjugations here: agent (mag-), causative (magpa-), social (nakikipag-), abilitative (nagkaka- and na-), qualitative (also na-) and then pang- and pag- which create gerunds. I can give you a basic layout of these in their respective aspects, where CV~ stands for the reduplicated first syllable of the verb or adjective root. Agent mag- is used to focus on the doer of any verb/action. Imperative/command: mag- Past: nag- Present: nagCV~ Future: magCV~ Causative magpa- focuses on the agent that caused an action to be done. magpa- nagpa- nagpapa- magpapa- Social makipag- focuses on plural actors of the same action simultaneously. makipag- nakipag- nakikipag- makikipag- Abilitative magka- focuses on the doer of an action, specifically on their ability to perform said action. magka- nagka- nagkaka- magkaka- Abilitative ma- focuses on the action that the doer had to ability to perform. No imperative form na- naCV~ maCV~ Qualitative ma- focuses on the state of the actor or object taking on a state of being (adjective). No imperative form na- naCV~ maCV~ Gerunds formed with pag- and pang- are abstract nouns from verbs. Pang- gerunds are specifically habitual actions. When used with mag- forms of verbs, you would form a gerund using pagCV~, while pang- gerunds are formed from agent focus mang- verbs.

You may find some, if not all, of the explanations you are looking for on this site: http://www.phrasebase.com/archive2/tagalog/tagalog-prefixes.html