yes, just use the correct ciosmaps and folder in the installer.
The base is the IOS used as base for the patches.
For example, if you use "249 base 56" it means that it's using the official IOS 56 as "original IOS", then some patches are applied to that files to add functionalities (usb2.0, re-add signing bug, NAND access rights, etc.), and the resulted files are saved in slot 249.
The slot 249 (which is only a folder named "249" on the Wii flash drive) contains the copy of IOS56 with these patches, it's what is called a "patched IOS" (or for most users a "custom IOS")
slot 236 usually have the patched IOS36 (used by a lot of guide to softmod the Wii)
The IOS used as base is important as it's the one having functions needed for the game. Some games require specific functions, like USB accessories support (Wiispeak, Wii tablet, etc. use IOS58), or hard drive access.
Call of duty require IOS 57, so the game when launched from an USBloader require a base 57 to allow the game to find the function originally found only in IOS57.
90% of games work with a base56 (probably because that IOS has all the functions that all previously released IOS had. Above IOS (57, 58, 59) have specific functions, and I guess they don't have all the other IOS functions in them, only the function needed by specific games, like
Dragon Quest X)