I know this post is old and most of you have figured it out by now but undoubtedly since I found it on google, someone else has/will as well so I decided to update it. You can pump the liquid into a smeltry (and probably other liquid accepting devices) and then output blocks and ingots from there. How to get it into the smeltry is left as an exercise for the reader. I have the following setup:
Yellowium ocean:
1x chunkloader to keep the world loaded
1x pump to pump out the yellorium into an ender tank
1x ender tank linked to one in the overworld
1x power supply (solar is great if you created a world that's always sunny, throw a battery there if not)
1x fluidduct to get from pump to tank
Overworld
1x ender tank linked to one in yellowium world
1x smeltry drain attached to the smeltry
1x fludduct to pump yellowium into smeltry (you can use as many as you want depending on the distance between the tank and the smeltry drain)
1x liquid transporter pair (this automatically pulls the yellorium into a basin to create blocks)
1x basin
From there, you can do whatever you want to get it into the big reactor. I use an elaborate setup of itemducts that pushes yellorium blocks into my reactor, pulls cyanite (sp) and converts it into yellorium then pushes it back into the reactor.
In lieu of a full on smeltry, you can also pump the yellorium into the tank, and then attach a fluidduct between the tank and a smeltry basin. This will output the yellorium from the tank into the basin and create a block. Then you can route it however you wish.
There's likely 100 or more ways you can deal with it. If you find an interesting way, please update the post as it's helpful to others that are looking.