Well, you can control the electron occupation number of the n-type dot by doping, but you will most likely not be able to change it once your sample is grown unless you are using some Schottky diode like setup, which would again be using some kind of leads. So it is just the general, not the momentary occupation. I do not know for sure about QD molecules, but my former office neighbour used layers of singly charged QDs for some experiments. I will have a look, whether I find some detailed information about how it was controlled that the QDs were indeed singly charged.
Edit: I do not know, whether this is what you are looking for, but I found some short description of the kind of doping used for growth of the singly charged QDs in one of his paper. See the (freely accessible) supporting online material of A. Greilich et al., "Mode Locking of Electron Spin Coherences in Singly Charged Quantum Dots", Science Vol. 313. no. 5785, pp. 341 - 345 (2006)
Otherwise I could just direct you to some groups working in the field of coupled QDs. As far as I know, the most prominent work in terms of QD molecules has been done by the naval research labs in washington. For example M. Scheibner and D. Kim should have some papers on this. However they are more into quantum gates. Pioneering work concerning the growth of such structures has been done in the group of A. Forchel in Würzburg a few years ago. Here the papers by M. Bayer from his Würzburg times and maybe also some from his own group later in Dortmund might be interesting. From the theoretical side I am not so sure, but papers from T.L. Reinecke and P. Hawrylak might be a good start.