Custom texture uploaders must always either specify which slot their costume goes over, or include all the files within the costume's folder, to ensure usage is optimal. After that, you may use TexID Fix to choose which slot you want your texture in.
First, you need both your Model.nud and Model.nut files in the same folder as TexID Fix. Then, you must open the batch file. Now it'll ask you for an ID, and you may choose a number between 0 to 255. Remember that the default costumes within Smash all use the 00 slot, while the last one (for most) uses the 07 slot.
After it's done, you may pack everything in Sm4sh Explorer, and it should display all costumes without a single clash