When we sit down to the seder, among the most important mitzvot that we fulfill is eating matza and maror. Our tradition is to first make the appropriate blessings (ha-motzi and al akhilat matza) on the matza, then to make the blessing on the maror (al akhilat maror – the blessing of bori pri ha-adama having already been recited on the karpas – see the discussion on the last daf, and finally to make a sandwich from them together, reminding us of Hillel’s tradition during Temple times.
This tradition is based on the conclusion of our Gemara, which points out that Hillel was of the opinion that ein mitzvot mevatlot zo et zo – that two mitzvot done together do not negate one another. That is to say, that the commandment to eat matza (or maror) does not need to be done on its own and can be done in conjunction with another commandment. Hillel argues that this is the intention of the passage (Bamidbar 9:11) al matzot u-merarim yokhluhu – that the Passover sacrifice will be eaten together with the matza and the maror.
The Aruk points out that this will only be true if both of the commandments being fulfilled at the same time are on the same level – that they are both Biblical commands. If, however, one of them was on a lower level (for example, if one of them was only a Rabbinic obligation), then it is likely that we would rule that they could not be done together. Since the accepted halakha is that since the destruction of the Temple – with the korban Pesah no longer being sacrificed – maror is only a Rabbinic obligation, we can no longer eat matza and maror together. Thus we first eat them separately and only afterwards eat them together as a remembrance of what Hillel did in the time of the Mikdash.
This point is actually made in the Gemara itself, where Hillel is quoted as saying that in our day eating matza is a Biblical command while eating maror is only Rabbinic, so the two cannot be eaten together.
Rav Ya’akov Emden points out that that this Hillel quoted by the Gemara does not appear to be Hillel ha-Zaken, Shammai’s contemporary, head of the Sanhedrin, who lived during the time of the Temple. More likely it is his descendant, one of the last nessi’im of the Jewish community in Israel, who established the set calendar that is still used to our day