If you use jaffas you will have to cook the skins for a much longer time, or they will remain very hard. With Sevilles the skins are always supposed to be cooked ( even if you strain the skins off at the end to make a jelly marmalade) but jaffa skins are always expected to be thrown away, so the growers do not care about the consistency of the skins of jaffas.
If you do add a liqueur to your marmalade, wait until the very end of the cooking, when the mixture is cooling before you pot it up, or else it will all evaporate if the mixture is very hot.