Do you mean, that when importing the picture it is resized and loose its transparent color?
One solution would be:
1) to size your pictures to the right size
(some softwares like like Irfanview allow batch resizing of many files)
2) to set the transparent color
3) to transfer the pictures with an FTP client like FileZilla.
Your must place your pictures in subfolders of /assets/galleries, where each subfolder is named according to the document ID. For instance:
for the gallery to be displayed on page 123.
4) to create your galleries manually by adding record manually the 'modx'_maxigallery table (where 'modx_' is here the table prefix you chose when installing MODx).
I've not tested it but its possible that your pictures are already to the size that they will have in MaxiGallery, they would not be resized when loading them in MaxiGallery. Else, you could maybe modify the source code to allow this behavior.