Some protocols uses an additional step of extraction by an equal volume of water-saturated ether to remove traces of chloroform, however, that is unnecessary and may be harmful. Precipitate DNA using either ethanol or isopropanol. The upper phase is normally the aqueous phase, however if the solution has high concentration of salt or sucrose, it will form the lower phase. Hydroxyquinoline is also useful because it is a powerful anti-oxidant which prevent oxidation of phenol. However, if you are glutton for punishment and want to prepare it yourself, look up the Maniatis book.
Phenol is highly corrosive and can be absorbed through skin.
Therefore take appropriate precaution when using it. Old chloroform solution may generate phosgene. Therefore use a larger volume of lysis solution. Temperature of centrifugation may be important for separation.