It's a bit tricky.
You can charge 2 cells in series just from the outermost connections, ending the charge at a total of 8.4 volts for the pair etc.
The downside is you can get problems with imbalance between the cells, where one is already full and the other is still discharging and such. Using protected batteries doesn't make this better: the 'good' protected cell will cut out of circuit when full, leaving no path for current to go through the other one that isn't full yet.
The upside of protected cells is that the weak cell will not over-discharge or even become reverse biased since its protection will open the circuit when the cell voltage drops too low.
Given all of that: yes, you can do this with protected cells to some degree. You could top up or recharge 2 cells in series from only the outer terminals several times without much of a problem.
You should, however, take them out and charge them individually every say 10 cycles or so to keep them balanced.
The only way around this is to build the charge circuit into the unit with access to the middle tap that interconnects the cells. It seems this is not possible in your host, so i'd go for the charge in series, take out to balance once in a while approach. This should be fine for a host that has a charge connector but also removable batteries.