How Does Connecting a Battery in Series Affect Current Flow
In the simple series connection, the current will be limited to the current from the battery with the lowest current rating. Note: that may not be the smallest of the batteries, either in physical size or in total energy storage. Just for example, Nickel-Cadmium batteries generally have very low internal impedance, so even a fairly small NiCd battery usually has quite high current capability (but will discharge very quickly at maximum current capability).

When batteries are connected in parallel, you add together the current capabilities of the batteries.

For your series/parallel connection, you'd want to connect at least enough of the smaller batteries in parallel in match the current of the larger battery (or at least to match the current requirements of your circuit). If you connect more in parallel than that, you'll get the same total current flowing, but less through each individual battery, so they'll discharge more slowly. That'll give longer battery life unless current draw is so low that the batteries are already limited by their shelf life (which is unlikely where they're powering motors and such).

In most cases, however, you want to ensure that any batteries you connect in series are as close to identical as possible--regardless of overall current capability, if some of the batteries discharge at different rates from others, things can get fairly ugly.