Never heard of coppercube and while it appears to be an engine I don't know that it was ported to the DS (the current website nor
https://web.archive.org/web/20090428114743/http://www.ambiera.com/coppercube and following snapshops appear to mention the DS either).
Games using custom archives on the other hand is well documented, and that can include sticking audio files in them (though that is actually quite rare) which vgmtrans and such will probably just search for the format header and rip it from that instead.
I have not got time to go looking at the game right now (don't think I have pulled it apart before but something is ringing a bell). Usual way to pull such formats apart is either to look at them and figure out what is going on (you need a means to tell where the files are, usually pointers or file sizes, and everything else is so much bonus content but often includes names, extra data (subdirectories, compressed vs not and plenty more in actual formats rather than archives), sizes (pointers are great and all but if you can read a size rather than calculating it then so much the better) or to find a known file (
https://www.romhacking.net/documents/[469]nds_formats.htm , indeed if SDAT is hidden in there somewhere that is a good choice of file as it will likely be large and not compressed ) and figure out what references it and move sideways from there.
Crystaltile2 then.
On the left are settings. The four most useful ones for most DS work are tile height (how many rows before you start a new tile), tile width (how many columns as it were before you start a new tile, though there is also how many tiles before it starts a new line), location (which you can also set by double clicking in the DS file system window, the DS icon on the top right of the buttons bar brings that up. Also in the status bar on the right I think it was it tells you what file the cursor belongs to) and tile mode -- different consoles use different modes of displaying graphics with the DS following on from the GBA in using mostly GBA 4bpp and 8bpp (1bbp and Xbpp are rarer, 1bpp normally only being seen in fonts as technically it is a type of compression). Others certainly have their uses and what help to make CT2 one of the better tile editors out there but cross that bridge as and when.
You can also play with the shift button and arrow keys to change various options.
Game console graphics are rarely a list of pixels of specific colour, instead it is more like paint by numbers where you have a key (palette in gaming parlance, hence palette swap for same graphics on enemy but different colours). Where you find the palettes is a big trick. You can use premade ones and hope you find something (often work well, especially the gradient ones), rip it from memory when the data you want is active, find it in the ROM (take said memory data and search the ROM for it -- palettes are usually too small to bother compressing, and tend to also be nearby to the graphics they deal with) or maybe have it loaded in (see NCLR in the known formats link before). If you find the palette you want in the ROM (or you injected it in somewhere) then you will have to visit the hex window, down the bottom of the options will be data-palette and palette-data, these will respectively grab the data from where you have the cursor and put it in the palette and take the palette and put it in the data.
You can also export the image and try to edit it in a more conventional editor before importing it back but know what you are doing there (see indexed images, and you will want to import the palette, that or know exactly what you are doing and make sure you don't use gradients or anything like that which create new colours unless you are also willing to encode said new colours in the palette and deal with any fallout from that).
I have a few more worked examples in
https://gbatemp.net/threads/gbatemp-rom-hacking-documentation-project-new-2016-edition-out.73394/
