The shot of the Lagoon is Sentai footage and then it cuts to new footage of Loki, Diabolico and Vypra.
The shot of Aquafiend rising and walking out of the Lagoon is Sentai footage. It then cuts to new footage once you see Diabolico and Vypra.
Here's Diabolico and Aquafiend
After Marina warns Chad that the Demons have stolen her Father's Staff, it then cuts to Sentai footage of Aquafiend being underwater. After Aquafiend says "Drain" while underwater, it then cuts to a surface shot of the water where it appears that water is bubbling. It looks like this surface shot is apparently new footage.
These shots     are back to Sentai footage.
The shot of GoBlue with his visor opened is actually kept intact in this episode but they make the footage darker in order to make it harder to see what actor is within the suit.
These shots   are back to new footage and then once it cuts to the underwater shot of King Neptune's Trident then it's back to Sentai footage.
These shots of the Red Ranger   are back to new footage.
Once it returns from commercial break, it then stars in Sentai footage with the Green Ranger firing his Blaster at the various Batlings however once you see the Red Ranger fighting Batlings, that's new footage but then it cuts to Sentai footage of Aquafiend being underwater.
This shot of the Blue Ranger with King Neptune's Trident is when it goes back to new footage.
After the Red Ranger catches the Trident and puts it down, it then cuts to Sentai footage of Aquafiend coming out of the Lagoon.
This shot of the Yellow, Blue and Red Rangers is back to new footage.
This shot is when it goes back to new footage.
Here's new footage of Giant Aquafiend  
Here's new footage of Giant Aquafiend, this time with King Neptune's Trident
Once you see the stock shot of the Omegazords exiting out of their Supertrain compartments then that's when it goes back to Sentai footage.
All remaining Giant footage is Sentai footage.
The next shot of the Rangers on the ground is the start of new footage.

Following info comes from GoGoV Episode 41.
Here's Aquafiend  
Here's Giant Aquafiend
Here's a shot of the Giant battle between Aquafiend and the Omega Megazord