Hi Tony
though your question is not so clear, my best answer is below: since only 3 month multiple entry visa is available at that time, you now just can stay in Vietnam for up to 3 months (unless you get a further extension).
regarding your Philippines visa question, there is NO visa on arrival for Philippines, you will need to visit Philippines embassy either in US or Vietnam to have it done beforehand.
you will need a multiple entry visa if you return to Vietnam and enter the country again (if not, single entry is enough)
hope the information above is helpful.