Head + Hands:

Simply Decompress the tiles at the given offsets within the utility and open them with the included mapping asm files and palette bin file, to SonMapEd. 

Export the result as a bmp, modify to your liking (Remember don't change anything in the purple.) 

Reimport over active frame in SonMapEd, and save Uncompressed tiles.

Recompress and insert newly compressed bin into the rom using a hex editor at the address the original tiles were ripped from.

City + Blue Flames:

Just like the Title Template, Decompress the tiles using the compression tool and open with SonMapEd.

Use enclosed City_Palette.bin and Flame_City_13tall_25wide_Mapping.asm to get the layout mentioned in the tool "More Info" section.

Export as .bmp and modify to your liking. Remember to leave the top left 8px x 8px tile black.

Re-import .bmp into SonMapEd over existing and save new tiles.bin.

Recompress the new tiles.bin file and insert into ROM at the same location the original was extracted with a hex editor. Remember to make sure the location after the last byte of the new tiles.bin is "00"

Use the Compression Tool to extract the mapping from the ROM (Tool shows the location for the respecting ROM type.

Open the resulting decompressed file with a hex editor and modify the mapping the same way you would the title. (I've left a mapping file "City_Mapping_Uncompressed.bin" as either a reference of how it should look, or you can just use it.

Recompress the mapping file using the tool and copy into the ROM at the address of the original mapping.

**Note: If anyone wants me to create a mapping of the tiles where you can just modify the city tiles just PM me on Romhacking.net.