For water, use a pump. That's what it's for...
For lava, well, it's slow. You can use a pump and replace the block of lava underneath every time it's pumped, but it would be quicker to just do it with the one at a time method. I would like to see the IC2 pump act more like the BC pump, which draws liquids from farther away that the block just below it. It would make the machine a LOT more useful, and a little more realistic.
Is there a reason for not being able to fill a cell directly like a bucket?
Buildcraft 2.2.0 handles this problem quite nicely... While you still have to bucket click BC Tanks, you can pump/store lava in them, and click them underneath a IC^2 Pump so that the Pump auto-scoops the created lava block into an empty fuel cell.
Sure, it's not automatic, but then again it's a niffy method of harnessing alot of lava in a short time span. I'd also suggest Zeldo's teleport pipes with this as well, since they can pump lava's long distance to a 'lava storage site' that can process the farmed molten fluid later...
Example:
|_| IC Pump |_|_|........... Pipes
|_|^ lava ^ | BC Tank| ============ | BC Pump|
...................................................||
*Note: When creating an empty space underneath the IC Pump, you'll also need either a half-block, or a RP chopped block to keep the lava from accidentally flowing in front of you as you click said tank.
I got a better solution, why not make it possible to fill a cell by simply right-clicking on a source block. Or better yet make it so when you hold a stack of empty and click on the liquid, it takes a single cell out, fills it, and places it in a different stack.
I can not take credit for this idea for it has already been thought up. In fact Alblacka has even thought about including it in the official mod.
Here is the link to the post.
I got a better solution, why not make it possible to fill a cell by simply right-clicking on a source block. Or better yet make it so when you hold a stack of empty and click on the liquid, it takes a single cell out, fills it, and places it in a different stack.
I can not take credit for this idea for it has already been thought up. In fact Alblacka has even thought about including it in the official mod.
Here is the link to the post.
This I want but maybe they don't want it this easy 
miner allow you to fill lava, but its bugged hard and need 2 pumps to work.
I got a better solution, why not make it possible to fill a cell by simply right-clicking on a source block. Or better yet make it so when you hold a stack of empty and click on the liquid, it takes a single cell out, fills it, and places it in a different stack.
Maybe it was not the case before version 1.23, but I can totally fill a stack of empty cell by right clicking a water source now.
use MobilePump addon, add tool that allows you to fill a cell with a rightclick using small amount of energy ( stack per 10k EU from BC tank, dont know how much from water source)
for automated way there's already pumps in IC (no to mention weird scheme of BC pumps, autocrafts and bukitfiller)
If you are using RP2, and I dont see why anyone who uses IC/BC would NOT use RP2 there is an amazing solution
After I setup the factory and left for a bit I came back and all 640 of my empty cells were filled up 
Allow me to elaborate.
Around lvl 10-13 there is usually GIGANTIC lava pools. Setup a BC pump there, with a bit of work you can have steam engine operating the pump, being powered by the very lava it collects. Send the lava you collect to your processing area, wherever it may be. Basically you connect the waterproof pipes to a tank for storage.
Next, you connect a deployer to the tank and keep it filled with empty buckets (ill explain how to)
Connect filter to the deployer and set lava bucket as filter
Connect the filter to a chest with pneumatic tube (all your lava buckets will go there)
Put all your empty cells in the same chest
Put automatic crafting table next to the chest with the lava cell receipe as filter
Finally, connect another filter to the chest, this time with empty bucket filter and send all the empty buckets back to deployer with tubes.
The way this works is deployer "right clicks" the lava tank with a bucket, filter pulls bucket out to chest, automatic crafting table using the stuff from chest makes lava cell, empty bucket gets sucked out by the 2nd filter and sent back to deployer.
I used the same method for water cells, then linked up the water cell output to extractor and created all the coolant cells I needed to make my 6 chamber reactor + its contents
Hope my explanation was clear enough, gl.
