I got a 12V motor, and 2 batteries.  I'd like to use both batteries in parallel to give longer run time without having to mess with moving wires around.  Now when it comes time to charge, will I have to remove the connections between the batteries?  They aren't the same group of batteries, one is a 24 and one I believe is a 27 group.

Thanks.

You can charge them the same way if that is how you are using them. Most will tell you that you have use the same size and make but if you are going to just use them up until there done then just do it the way you said you were.

There is no problem using unmatched batteries in parallel.  That is only a concern if you are using them in series.