There are probably many ways to tune a sitar and every good player will tell you that you should tune by ear, which is certainly something you should work on developing, but this can be difficult when you are starting out. Once you have the sitar tuned properly it should be fairly easy to make small adjustments because you will hear the clashing sound compared to the pureness of a well tuned sitar but if you have never tuned your sitar to Just Intonation this is how we can start, there is quite a lot to do. Don't rush it and don't get frustrated, it sometimes takes a while until you get used to the process.
So where to start with all those strings? This may not be the 'proper' way to start but it will get your instrument in tune. Start with the taraf strings. These are the sympathetic strings that lay underneath the main set of strings. These are tuned to the raga that you are playing in, the intention is that they ring out on every note you play in the raga. I will be writing out raga yaman so I will show you how to tune to this.
There are a many ways to tune these strings, depending on how many taraf strings you have and which school/branch of tradition you are taught in, amongst other things.
This is the way I tune my sitar, it has 13 taraf strings but some sitars have 11. Going from the longest string to the shortest:
N, D, S, S, R, G, G, m, P, D, N, S, R (remember that the Ma is sharp).
If you have 11 strings you could try this:
N, D, S, S, R, G, m, P, D, N, S
Tune these using Wintemper or whichever Just Intonation tuner you want to use. It may take a while as you might pluck the wrong string, or turn the wrong peg, or you might find that the pegs are fiddly and physically hard to turn. If they are hard to turn just detune it with a slight pulling upward pressure and then tune up again, pushing down when you get near the right note. Try to tune the string exactly to the right frequency, the sitar will sound beautiful if you get it right so take your time and get it perfectly in tune.You may need to go back and check these are still in tune when you have finished because the pressure of tuning one sometimes changes another but do this until it is correct.
The Main Strings
Now for the top strings. Start with the jor string. This is the second string from the bottom as you are looking down on the strings from the playing position. Tune this to Sa. You should hear the taraf strings ringing when you get close to the right tuning but make sure that it is exactly in tune. This is a very important string so make sure you get it accurately in tune. You can use harmonics to check, this is sometimes easier to hear. Touch the string about halfway between the bridge and the nut at the neck, and should be around the 11th fret. Pluck the string while your finger is touching and you should hear a chime sound, you may have to move your finger to find the sweet spot. Check this frequency against the taraf and/or the tuner.
Now the next string. Tune the next thickest string. This should be tuned to Ga. Go through the same steps as the jor string.
The next thickest is tunes to low Sa. The easiest way to do this string is probably to play the jor string and then this thickest string. They need to be tuned to the same note but an octave apart so you should be able to hear the wobble/dissonance if they are not in tune with each other. Make sure you get this low Sa string accurately in tune because it will make everything sound horrible if it's not dead on.
The next string up should be a similar thickness to the taraf strings. This goes to Pa. Again, get this exactly right.
The last two strings tune to Sa, with last one an octave higher than the other.
The string we missed out, the first (bottom) string, needs to go to Ma. Now this is natural Ma, not the sharp version we used for the tarafs. You can use harmonics for this one. Pluck the 11th fret harmonic on the 2nd string and then hit the harmonic on the 7th fret on the first string. Adjust the first string until it sounds pure and completely in tune, no wobble/dissonance.
Now you have your sitar in tune! It would be wise to go back and check all the string again, just to make sure none of them have slipped out of tune while you were doing the others. It should sound beautiful and sing out when you pluck the strings (with your mizrab).
The last thing to do is to adjust the frets to make them in tune with the tarafs. This is very important because if you don't then when you play a note it won't ring out and sound beautiful, which is the whole point.
The first thing is to make sure your first (Ma) string is EXACTLY in tune. Check this by plucking the 7th fret harmonic and then plucking the Sa taraf string. When it is exactly in tune pluck the 7th fret harmonic again and then play 7th fret. These two notes should be exactly in tune with each other, just an octave apart. You can play the 7th fret note and pluck the taraf to hear a comparison. Move the fret to make the it exactly right.
Do the same thing on the 17th fret. This is an octave above the 7th.
Now go back to the 8th fret and play the note (first checking the Ma string is in tune again). Pluck the Re taraf to and move the fret until it is exactly in tune with the taraf. You will hear the taraf ring out when it is in the right place.
Now skip a fret and repeat the process with the 10th fret. This is Ga so pluck the Ga taraf and check this. Move the fret to get the Ga taraf to right out.
Skip another fret and go to the 12th fret. This is Ma tivra (sharp). Go through the same process.
The next fret is Pa. Again, the same process.
The next fret is Dha (14th fret). Same process, move the fret until it is exactly in tune with the Dha taraf string.
Skip a fret to the 16th fret and this is Ni. Same process again.
The next fret is high Sa. This should be already in the correct position. The next fret is high Re, and the one after that you can adjust to high Ga.
Go back down to the 1st fret. This is low Ma tivra. The 2nd fret is Pa. The 4th fret is Dha and the 6th is Ni. These last two should be checked against the first two (longest) taraf strings.
All of these frets listed should make the taraf string ring out when you pluck them. The important thing when doing this fret adjustment process is to make sure the Ma string is exactly in tune before you go to the next fret.
Now you're finished, your sitar is in tune according to Just Intonation and raga yaman is ready to play! It should sound beautiful now.