Were the books in .epub format and without DRM? If so, you should be able to just put them in the import folder inside your ebooks folder (these should be created on your SD card when you install Aldiko) and then import them from within Aldiko. If Aldiko cannot import them but works OK otherwise, I wonder if the file format is incorrect.
If you are using Calibre to manage and convert your books, you can also use the "save to disk" option to put them in the import folder.