Jagganath and Krsna are the same, so when Krsna is with His brother and sister, He is known as Jagganath, and when He is with His village girl-friends, He is known as "Radha-Krsna with Gopis."

Srila Prabhupada - "Regarding your question about Lord Jagganath and Lord Krsna, Jagganath is Krsna.

Krsna's childhood ages up to His 15th year He lives in Vrndavan. 

Radharani is His childhood friend. But Krsna, after returning to His father's home at Dvarka, came to see Kurukshetra during some solar eclipse. 

At that time His sister Subhadra and brother Balarama also came in a chariot, and this incidence is worshipped as Jagganath Ratha Yatra. 

The conclusion is that Jagganath and Krsna are the same, so Krsna when He is with His brother and sister, He is Jagganath, and when He is with His village girl-friends, He is known as "Radha-Krsna with Gopis." 

So Whomever you worship, it is the same, but if you like to worship Jagganath you can continue and it is as good as worshipping 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. 

Vyas is the Spiritual Master, therefore the Spiritual Master is the representative of Vyas. Therefore the Spiritual Master's seat is called 'Vyasasana.'" (Letter, May 15, 1970)