Not sure what you mean by a 6 volt cell so assume you mean a 6 volt
battery. The 2 individual 6 volt batteries are probably wired in
series which is perfectly good engineering. In fact that configuration
has a significant advantage over a single 12 volt battery. That is
that the batteries can be linked by a fuse that is, in effect, internal
to the battery and protects it from terminal shorts. I used that
configuration for years.

2 6 volt batteries in series will behave like one 12 volt battery as
far as charging is concerned. Only the packaging is different.

If you really meant parallel perhaps you could describe the
configuration in a bit more detail.

Andy