Paralel charging two Lithium Polymer batteries on a MP3 player Colorfly C4
2 1.8Ahr cells in parallel is the same as 1 3.6Ahr.  Its called a 1s2p cell.

Sometime LiIon chargers stop charging after a fixed time.  Something like the capacitry / charge rate * 1.5.    So you might not end up with a fully charged pack after a single recharge.  

Using a single cell LiIon batteries in parallel (with the same specifications and age) is generally acceptable.  

When they are initially connected though, you need to make sure they're nearly at the same voltage.  When connected the current flow will be I = (V1 - V2)/(ESR1 + ESR2).  So long as I is less than the peak discharge and charge current you're fine.

If the batteries have the same specs, there is nothing more to worry about.

If the batteries are different (but operate over the same voltage range) then one just needs to make sure that during charging the current sharing doesn't violate the charge rate of 1 cell.

Even have a multicell stack, putting them in parallel is fine.  But here it is a bit more tricky as the stack needs to be connected at the cell level, and the parallel capacity of each cell in the stack needs to be nearly identical.