Their jewellery is personal, there's nothing that belongs to the state or, as far as we know, to a private foundation they set up. So yes, many pieces are Sofía's personal property. There's a special set (diamond tiara, earrings, brooches, necklaces and bracelets and pearl necklaces and brooches iirc )that is reserved for the sole use of the Queen. These jewels, like some others, specially the more historical, belong to the head of the RF (now Felipe) and are Letizia's to use as she chooses. Other jewels belong to JC, and it's very likely that he'll leave them for Felipe and the main line. (for example Queen Maria Cristina pearl and diamond tiara or the Cartier Pearl and Diamond tiara)
Letizia has her own jewellery (earrings, bracelets, necklaces...) and will probably inherit (through Felipe) part of Sofía's collection. When she was the Princess of Asturias Sofía lent her tiaras and jewels, it's very likely that she's still able to use pieces from Sofía's collection. And many of Sofía's pieces belong to JC/the SRF and are probably at Felipe's disposal.