Phoneme Analysis Question

Hey guys,

I'm working on describing the phonemic inventory of a language, and I've got
a (probably stupid) question:

   If two phonemes have the same phonetic realization in a particular
environment, how do you determine which a word has if it has that
environment?

Consider "fair, bear, chair, hare, very".  In my idiolect at least, short E
and long A are two separate phonemes, but before R they have the same
phonetic realization.  I realize this isn't the case for many of you, but
it's just an example.

Or consider the T phoneme being realized phonetically as a D after a
stressed vowel and before another vowel (again, in my idiolect, I realize it
doesn't apply to many of you).  In the word "atom", it's phonetically D, but
in "atomic", it's phonetically T.  This one I can confidently assign to the
T phoneme, in that I have a variant of the word with the D-realization
environment and a variant without.  What about a word where I don't have a
varying pair like this?  (And where the spelling doesn't indicate a
historical pronunciation before merger...)

Sorry for the long-windedness, but I'm not sure of an easy way to explain my
dilemma.

Thanks for any help,

Joe Fatula

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