You can't mix and match 3s with 2s2p and expect good results. If you just mean these are the two configurations you are considering, ie either 3s or 2s2p that's fine.
With the 3s configuration there's no need for a fuse unless your string of panels can provide more current than your charger can accept. If your string can produce say 5 amps and your controller can accept 10 amps, you want that full current to be available to the charger so in practice there isn't a fuse that you can use here that will give any practical protection since it will never blow.
With 2s2p there's no need for a fuse in line with the strings since you only have two. Even if one string faults it will never get more current that it can handle or produce. The fuse has to be rated to carry the full current out of the string, and since there is only one other string which produces the same current there is no circumstance in which there will be enough current to blow the fuse on the faulting string. If the array can provide more current total than the charger can accept a fuse between the array and controller is appropriate.
Hope that hasn't been confusing.