I'll assume you have something like this:
simulate this circuit – Schematic created using CircuitLab
If you don't, then do provide more information.
When charging is a fuse needed? I'd say yes! Basically, fuse is there to protect the battery from being damaged by the load. Batteries can often provide large current when shorted and if somehow the load gets shorted, battery would be protected by the fuse from the short. If the battery is charging, and the load somehow gets shorted, then you'd have even worse situation. Not only would battery provide current for the short, but charger would as well. The result would be melting cables and damage to the battery and the charger due to overcurrent.
Next, about the "positive" part. That, as always, depends on perspective since voltage needs a reference point. I'd call positive terminal of the battery positive and I'd call the terminal of the charger connected to the positive terminal of the battery positive as well. They're both more positive than their own negative terminals and are commonly marked as positive, which means that others will easily understand about which terminal you're talking.
If you explained to us why you want to know which terminal would be which, we could provide more information. For example if you measured voltage between the positive terminal of the charger and the positive terminal of the battery, while the charger is running, you'll see that the charger's terminal is more positive than the battery's positive terminal (making the positive terminal of the battery negative). In such situations I'd still keep the designations I introduced in previous paragraph since changing them could add confusion into conversation.
Two fuses, for two reasons.
First, I want to establish some arbitrary values. For the purposes of the below, I will assume the devices will draw 1 amp while idle, be connected to either one 10 amp fuse, or two 5 amp fuses, and become damaged at 7 amps.
Depending on how sensitive these devices are, limiting the current draw of the two devices may not be sufficient to prevent one from becoming damaged. Imagine that one or both devices are idle when one device suddenly malfunctions. A short circuit causes it to draw 8 amps of current, well beyond the 7 amp damage-point. With a single fuse, the total amp draw is 8 + 1 = 9 amps, so the fuse doesn't blow and the device is damaged. With two fuses, the five amp fuse on the malfunctioning device blows, preventing further damage. This isn't a contrived scenario, most devices are in standby most of the time, and, although some malfunctions can cause sudden power spikes, others can cause slow burns. I could answer the question more fully if I actually knew what the devices were.
Another reason is that, depending on the nature of the devices (From your question, maybe high power electronics?), I could imagine that one may internally malfunction and destroy the other. I really couldn't say whether this was a possibility without more information, but I would consider it. With a fuse on each device, each device has its own protection and you don't have to worry about hooking up another device to the circuit, removing one device from the circuit, or changing the nature of one device. You can rest assured that each is separately protected from a surge. It's just good practice.
If this device is a low-cost device, a low power device, or a temporary situation, it wouldn't be worth the bother. I would say that if it was worth the effort of asking the question, its worth a couple of bucks for a separate fuse.
Best Answer
Use configuration 1. This will prevent damage if one of the batteries fails or is undercharged with respect to the other battery.
Also, you only need to stock one size of fuse, unlike in version 3.