I bought this asset, and now I'm going to use it now. 

I'm trying to work with Tiled, a map maker, but is it better to set the Width and Height of Tile Size to how many pxiel in new Map and work with it?

Hello, the tileset is a 48px tileset. However, the textures are optimized for RPG Maker, that is, with borders.

With 24px tiles you could also use it like this because with the 96px textures the inner 48px are the seamless texture part.