The best way to do this is to begin with the lowest string and set exactly the fret corresponding with the note from the next higher string, and tune this string with the produced note, otherwise the frets on that second string will be completely out of tune (this is of course not applicable for clavichords).
For a bass viola da gamba this means that the Csolfami (C) and Elami (E) strings in 1/4 comma meantone should be tuned as an exact major third, but in other temperaments not - e.g. in 1/3 comma meantone this third will result 1/3 comma smaller than the just one.

For the moment it is up tou you to decide what to do with slightly different places for the frets, if you give preference to some notes or prefer a mean placement.
In some cases it is very clear that the best option are double frets. For the bass viola de gamba in 2/7 comma meantone the first fret should be double: the first one for G# on the G string and for the C# on the C string, the second one for all other strings producing respectively Eb, F anb Bb.

You can use this utility also in reverse manner to find out the temperament from a given instrument with known fret distances by trying the different temperaments, e.g. clavichords.

Note that this tool considers only the notes used before about 1600 in the iberic music. In most ancient temperaments these notes cannot be used enharmonically. The option for more notes, temperaments and frets will be later added.