If you wire in series, you add the voltage but keep the capacity (mAh) the same. If you wire in parallel, you add the capacities but keep the voltage the same.
If you did the QFM mod and got increased capacity but it went slower (due to extra weight of 2nd battery) then you may have wired in parallel by mistake. You want to wire in series for extra speed. In effect, the batteries should be end-to-end when wired; they don't necessarily have to be touching end-to-end but should be connected that way.
A basic dual cell (series) mod would start with the negative, flat end of one battery wired to or touching the negative terminal (the one with the black wire), with that battery's positive, button-top end wired to the negative end of the second battery. That second battery's positive end should then be wired to the positive terminal (the one with the red wire). You can arrange the batteries however you like, but that's how they need to be connected.
If you don't want to mess with all that, why don't you try
The Layman's Dual/Tri Cell Mod?