Refilling fountain pens

For any serious writing I prefer to use a fountain pen. I have used one since secondary school and I continue to prefer them even though they now appear to have fallen out of common usage. However, I have a problem that must have a well-known solution even though it eludes me:

When I come to refill the ink from the bottle, as I twist the plunger at the top end of the cartridge its other end must remain below the surface of the ink. With a small ink bottle that is only partially full my fingers are struggling to be low enough: the cartridge is only so long so the neck of the bottle gets in the way.

How is this normally solved? Am I supposed to first pour some ink into a tiny bowl then fill from that?