I have battery holders which can support 3 AA batteries in a side by side configuration. Typically, to save space, I keep the batteries inside the battery holder when they are not used. Is this a good habit it?
I have a picture attached below to make it easier to understand my layout. The connector is tucked underneath the battery holders so that they do not affect other components.
Take the mega & uno out and show another pic please, so we can see what you mean.
In principle as long as the batteries are not supplying current it will not matter that tey are in series; but if the ends are short circuited you have problems!
Looks like the battery box has flying leads with stripped ends. This may not be safe. If the stripped ends touch each other or some metal object, a short circuit will occur, which could damage the batteries by over-discharging them or even cause a fire! If the wires touch some circuit board, there's a chance they could damage that also.
If you wrap a piece of insulating tape around one of the wires, that would prevent those things, but there is a danger the tape could fall off.
Oh, wait, they are not rechargeables. Once discharged they are useless anyway. Please at least put them in a battery recycling collection bin when you are done with them. Preferably stop buying non-rechargeables.
If using rechargeable AA, you may need to get a 4x holder because the voltage is a little lower. But an advantage of this is that 4xAA can be used to power many Arduino directly via their 5V pins, bypassing the on-board regulator.
I have at least 16 of the AA batteries so it is likely that I will be using AA batteries for a fair bit of time. For powering an Arduino board, I personally use a USB smartphone charger connected to a wall outlet.
A tip for using multiple AA/AAA rechargeable cells in holders is not too mix brands. Ideally don't even mix packets, meaning use cells together that came from the same packet. Cells from the same packet will be most similar to each other.
If you mix different rechargeable cells, what can happen is that some will be slightly stronger/higher voltage/capacity than others, and as the cells discharge, the weaker ones will discharge faster, and can even get reverse-charged by the stronger cells, which can damage them.
I think I found a way to keep batteries in the battery holder without the risk of short circuit. I stripped off insulation layer from a stranded wire and pushed it into the connectors. A picture is shown below. Would it work?
I have attached 0.1" female crimp headers to some battery holders. You can then solder 0.1" pin headers to your PCB to connect them to, or use extra-long 0.1" pin headers for breadboard use.