The way to combine the two
According to Rabbeinu Chananel (Pesachim 115a), “one wraps the maror on the matza,” or, in other words, the matza is wrapped by maror. And that is what Sefer ha-Chinukh (Commandment 21) wrote.
However, the custom is to place the maror between pieces of matza, and that is what Arukh ha-Shulchan (475:7) and Kitzur Shulchan Arukh (119:7) wrote. In any event, both are equally valid (Haggadat Mo’adim u-Zemanim, p. 107).
Mishnat Ya’akov (475) explained that the Rishonim would use Romaine lettuce for maror, and they were therefore able to wrap the matza with maror, but in Europe they would use horseradish, and it is impossible to wrap matza with it, and that is why they placed the maror between the matza.
In reality, even though it might be appropriate to revert to the practices of the Rishonim and to wrap the matza with maror, in any event, since it is not essential for the fulfillment, it is the accepted practice to place the maror between the matza. In this way, it is possible to say that one matza is meant to commemorate the matza eaten with the Pesach sacrifice, and the second matza to commemorate the Pesach sacrifice itself (Vayaged Moshe, 26:7).
Dipping in charoset
According to the Ra’avya (quoted in Tur, 475) and Rabbeinu Yona (Seder Leil Pesach), it is not customary to dip the maror of korekh in charoset, as one has already fulfilled the requirement of dipping, and as the charoset is only optional, it will annul the requirement of eating matza with maror according to Hillel. Similarly, there is no need to offset the pungent taste of the maror (one of the reasons given for dipping the maror in charoset), as the matza annuls this taste.
However, according to Rashi, the Rosh (brought by the Tur ibid.), the Or Zaru’a (II:256) and others, the custom is to dip the korekh in charoset as well, because that was what Hillel did (because he would fulfill the obligation of maror with korekh), and we act as Hillel did in fulfilling korekh (Hagahot Maimoniyot, 8:7).
In practice, the Shulchan Arukh (475:1) wrote that one dips the korekh in charoset. The Rema (ibid.) noted that there are those who do not dip, while the Mishna Berura (subsection 19) wrote that the custom is to dip.
Shaking off the charoset
Regarding maror, the Shulchan Arukh (ibid.) wrote that one shakes off the charoset, whereas in regard to korekh, he did not write that one shakes it off, implying that there is no need to do so for korekh. This is indeed what the Beit Yosef (ibid., s.v. ve-khen katav) cited in the name of the Agur from the Maharil. However, the Mishna Berura (subsection 17) wrote in the name of the Ma’amar Mordekhai that one must shake off the charoset for korekh as well. In any event, whoever wants to eat the korekh without shaking off the charoset first may do so (see Pesach Me’ubban, 308; Kaf ha-Chaim, 475:32).
The maror in the korekh
The quantity of maror
The Sha’agat Arye (100) wrote that according to the Rosh, who states that the need for a ke-zayit of maror is only because of the blessing, there is no need for a ke-zayit for korekh, and the Yeshu’ot Ya’akov wrote the same.
In the final analysis, the Sha’agat Arye disagreed with the Rosh, and wrote that one is to eat a ke-zayit for korekh as well, and that is the ruling of the Mishna Berura (475:16).