I know what you mean, sometimes I get stuck on things I shouldn't too.
Treat cells hooked up in parallel like a single cell. Maybe tape them together or something to help you visually. Just remember to check they have matched charge when you connect the parallel cells initially.
After you group them in parallel sets, hook them up to the charger like a regular 2S cell, one wire from the charger plug on negative for the first group, another wire on the positive-negative connection between the groups, and one wire on the positive connection of the second group.
The point of a balance charger is charge each cell as if it stands alone so there's a channel dedicated to each cell in the series set. The first channel shares the high side connection with the low side connection of the second channel.
You'll have to check the pinout on the charger. The pinout is standard on those JST-XH connectors that come with the LiPo packs since the intent is to plug the cells right into the charger. Wire colors will depend on the extension cables you're using or if you're making cables yourself.
In terms of loading the pack while it's being charged with a balance charger, it's not an issue. Just like a USB charger, each channel is not adversely affected by the change in load. It simply goes to max rate when the battery is loaded then resumes normal charging when the load is no longer present.
I hope I answered your question, I'm kind of tired right now, pretty late, off to bed.