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It probably doesn't affect the charging cycle, but with the screw-ups lately from Apple's design teams, who knows. Lithium batteries are much more forgiving than lead acid or NiCad or NiMH batteries, especially in memory retention. It sounds like the underpowered charger you are using is trickle charging the MacBook. That is, charging rather slowly over a long period of time. Modern devices with modern batteries tend to be fairly cooperative with battery charging sources that are not an exact match to the one they provided in the box. I would make sure that it completely charges the battery every time though because what will effect a lithium battery is the total number of charge cycles it can handle in its life expectancy before it gives out. After you charge a lithium battery enough times, it will eventually wear out. So make the best of all those charge cycles by charging it to 100% capacity each time so you don't have to charge it again as soon. That cuts back on the charge cycles which ultimately extend the battery life.
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