I’m not sure what your level of familiarity is with the shamisen currently, so if I mention something that seems too basic, I apologize.
Essentially with stringed instruments, each string has roughly two octaves of notes, going from the open string to the highest playable neck position. So on Ichi no Ito tuned to C, you have C at the open or 0 position, which then goes through the rest of the notes before arriving again at the 10th position C. This repeats up to the 20th position C, with some room left to play higher notes beyond that.
This holds true for each string on the instrument. On a niagari tuned shamisen, Ni no Ito is tuned a 5th higher than Ichi no Ito (which is G, assuming a tuning of C for Ichi no Ito). The 5th here is relative to the major scale (i.e. 1, 2, 3, 4, 5, or C, D, E, F, G), which could be more info than you’re looking for at your current level but will be relevant for transcribing and playing as you become more advanced.
Where this comes into play is that once you hit the note of G on Ichi no Ito (6th position), each note on Ichi no Ito is now also present on Ni no Ito, but in a lower position. This carries up the Ni no Ito again and then repeats for the San no Ito.
When transcribing, if you want to vary the strings you’re playing, try taking all of the notes above the 6th position on Ichi no Ito, and moving them to the appropriate place on Ni no Ito. Once you’re comfortable with that, you can take any notes above the 4th position on Ni no Ito (which is C, or the open San no Ito), and play them on San no Ito.
An important thing to keep in mind with the shamisen is that each string has a very distinct tone. 10th position Ichi no Ito sounds nothing like the open San no Ito, even though both are the same pitch. The tone colors from each are quite different. When you’re transcribing, you may want to keep that tone color in mind, and choose note positions that help to capture the original intent and sound of the piece. Or, as you get comfortable, you might want to play around with more notes on the Ichi no Ito, to give the piece a jonkara type flair. It’s up to you, go with what you feel is best for how you’re hearing it in your mind.
Hope that helps.