Whereabouts in Egypt did they place Yosef's coffin?
Targum Yonasan: They lowered it into the River Nile. 1
Maharal (Chidushei Agados Vol. 2, p. 53, to Sotah 13a): One opinion in the Gemara is that his coffin was lowered into the Nile. (The Egyptians hoped he would continue to be the source of their food; i.e. that the Nile would be blessed in his merit. Thus, he was not buried among wicked Egyptians.) To another opinion, he was placed in the burial vault of the kings of Egypt (for it would be disgraceful to leave him unburied); but the precise location was not publicly known.
See Ba'al ha'Turim.
Why did they place Yosef in a coffin?
Moshav Zekenim #1: [Bnei Yisrael did so,] so it would be easy for them to take him when they would be redeemed from Egypt.
R. Bechayei, from Midrash Tanchuma (Beshalach 2): [The Egyptians] put him in a metal coffin and lowered it into the Nile, so Bnei Yisrael would never find him. 1
Moshav Zekenim #2: It was the practice to bury only kings in a coffin.
Seforno, Ha'amek Davar: It was Hashgachah that they not bury him, so his coffin would be recognized when they left Egypt. 2
Why did they embalm Yosef?
Moshav Zekenim: It is because he embalmed his father. One who eulogizes, he will be eulogized... (Kesuvos 72a). 1
Ha'amek Davar: It was lest his body rot.
This implies that Yosef acted properly. Rebbi (in Bereishis Rabah 100:3) says that Yosef was punished for this! Rabanan (there) say that Yaakov commanded his sons to do so. Ramban (48:7) connotes that Yaakov would have embalmed Rachel had he been able to. Teshuvas ha'Rashba (369, brought in Darchei Moshe YD 363) says that there is no pain or disgrace through embalming. The Radvaz (1:484) concludes that we should not try to alter the nature that Hashem established. Surely we cannot learn to embalming done nowadays, for perhaps it is different! (PF)