If I understand you correctly, you might have a score like this...
...and because there are only two voices notated and no guitar chord symbols in the score you aren't sure what chords to play to ad-lib a fingerpicking accompaniment.
If the music you are dealing with is Baroque or early classical style (my example above is from Handel), I think you could try taking an approach like a harpsichordist would have used to ad-lib accompaniment to an unfigured bass.
Look up "rule of the octave" and "unfigured bass" for detail. The basic approach is to play root position chords for bass notes of the tonic or dominant and then play chords of the sixth, either first or second inversion chords, on all other bass tones.
It can be tricky deciding how to treat an actual bass, because movement of the bass can be arpeggiation where the bass moved over chord tones but the chord doesn't actually change, or the music may change key in which case you need to reassess which tones are the tonic and dominant. But, if we try to apply the basic approach of root position chords on tonic and dominant and inversions on the other bass tones to the example above, we get...
^ before numbers just means scale degree so
^1 is the first scale degree, the tonic. I put the
^1 tonic and
^5 dominant in blue to show where we will use root position chords. The other tones are brown and will take inverted chords.
I put red boxes around what I considered to be the actual chord changes. This is where the bass arpeggiation idea comes into play. Notices that in the first bar the bass does change, but it's just an octave. The bass moved but the chord didn't change. Both tones are
^1 the tonic and so get a root position chord.
In bar 2 the bass continues with
^7. This is a really good example of bass arpeggiation. Instead of treating it like two chords, it probably makes most sense to consider
^7 as one
F7 chord. It's tedious to explain in words, but if you harmonized just the
^4 as a first inversion chord, it would be an
Adim/C, just hold that chord when the bass moves to the
^7 and the result is
F7 in second inversion. The other way to handling that part is just quickly looking at all the tones
C F Eb and seeing is an incomplete
F A C Eb or
F7 inverted. Again, much easier to just do with some practice than to put into words!
The bass continues to
^3 which being neither tonic nor dominant should take first inversion chord
i6. Next the
^2 has a rest in the treble so you could simply play nothing, or if you wanted to play a chord it would be first inversion
F#dim. Final the bass tones
^5 just take root position tonic and dominant chords
If it seems like that is a lot going on in a short span of time, or if the
D are confusing because of the key signature, just understand that the rule of the octave which I mentioned earlier would be the basic training to play most of the stuff in an intuitive, automatic way. This Google Site has an nice overview of that material.