Oddly enough amongst the Indic languages, Tamil has precisely the same problem: க, ப, ட may be voiced or voiceless plosives depending on context. Sanskrit loanwords in Tamil are typically pronounced very differently compared to their original in Sanskrit, or even in Telugu.
Personally when transliterating any Indic language I tend to use ISO-15919, and in that scheme, it is Rāma, and 'a' represents the schwa. Or Rāmaḥ, Rāmam, Rāmē, or Rāmasya, whichever grammatical attachment is appropriate.