This is a pretty difficult question to answer without having more information. The question you probably need to ask is why the LS2208 is rejecting those barcodes you are trying to read as barcode quality is the first place to look. You should also check if the optics lens is clean or not. Finally is it a problem with a single LS2208 or have you tried a couple with the same result. It is possible you simply have a dud unit as my experience is that the LS2208 work extremely well with 1D barcodes.
Also the LS2208 is a fairly old model and the new LI2208 is worth looking at which has better performance. If possible get someone on site to look at the environment and how you are using them.
However to answer your question about configuring the LS2208 you should use Motorola's 123Scan2 application. This is available at the link below.