If you have BIN/CUE files, use the chdman tool (part of the MAME suite) to convert them. Simply drag your .cue file onto chdman.exe (or use a batch script) to create your .chd .
For the search engine crawlers and the determined user, here is the exact workflow to ensure your metal gear solid spain disc 1 chd works flawlessly. metal gear solid spain disc 1chd work
The biggest issue with CHD is that emulators often see them as separate games. When you reach the communication tower and need to swap to Disc 2, a standalone CHD might leave you stuck. If you have BIN/CUE files, use the chdman