Regarding your question about Lord Jagannatha and Lord Krsna, Jagannatha is Krsna. Krsna's childhood up to His 15th year He lives in Vrndavana. Radharani is His childhood friend. But Krsna, after returning to His father's home at Dvaraka, came to see Kuruksetra during some solar eclipse. At that time His sister Subhadra and brother Balarama also came in a chariot, and this incident is worshiped as Jagannatha Rathayatra. The conclusion is that Jagannatha and Krsna is the same.
So Krsna when He is with His brother and sister, He is Jagannatha, and when He is with His village girl-friends that is Radha-Krsna with Gopis. So Whomever you worship, it is the same, but if you like to worship Jagannanth you can continue it and it is as good as worshiping Radha-Krsna. Krsna has so many forms, and which ever form you worship it is all the same, but you should worship that form which you like most.
Regarding the means of worship, our Vaisnava process is first offer respects to the Spiritual Master, then Lord Caitanya, and then Lord Krsna. Vyasa is the Spiritual Master, therefore the Spiritual Master is the representative of Vyasa. Therefore the Spiritual Master's seat is called "Vyasasana."