If you're taking care to write the readings over the characters they belong to (which people don't always do), then geminated consonants belong to the first kanji:
学{がく} + 校{こう} gaku + kō ＝ 学{がっ}校{こう} gakkō
As you can see, the consonant still belongs to the first kanji. Gak is a reduced form of gaku, having lost its final vowel u. Likewise, in your example you would split 一緒 into いっ and しょ.
Sometimes readings are assigned to entire compounds rather than to individual kanji. Although 今日 was historically compositional (ke + pu), these days it's treated as a 熟字訓 reading—a reading assigned to an entire compound, rather than made up of the individual readings normally associated with those characters. So in cases like these, it makes more sense not to try to split them up:
今日{きょう} kyō
In your last example, どころ dokoro is a rendaku'ed form of ところ tokoro. Just like with our earlier examples of がっ gak and いっ is, we'll write it the way it's pronounced, rather than trying to represent an "underlying" pronunciation with the /t/ intact:
居{い} + 所{ところ} i + tokoro ＝ 居{い}所{どころ} idokoro
Generally, you should write furigana with the standard pronunciation of the word you're writing, unless you're trying to specifically emphasize another pronunciation. Since Japanese spelling was reformed recently and is now relatively accurate, that makes things fairly simple.
You'll find that there are people who pronounce a few words differently than they're spelled. Normally, you would write:
女王{じょおう}・体育{たいいく}・雰囲気{ふんいき} rather than 女王{じょうおう}・体育{たいく}・雰囲気{ふいんき}
In these cases, I think it's better to write them like the left—unless you're trying to specifically indicate that you pronounce them like on the right.
