You won't be able to export .pxel or whatever files directly into Tiled. It is not a known format.
1. Export all your files from your editing programs as .png/.gif/.bmp...etc
2. Open up Tiled at the top find the Map pull down. Click on "New Tileset" (Map->New Tileset)
3. This will open a prompt asking you to both name the tileset as well as select an image, which is your tilemap you made in pyxel edit or gimp, but saved in .png/.gif/.bmp....etc formats.
3. Also set your dimensions which is the size of each individual tile, and your margins which is the space that separates your tiles(Which can be zero)
4. Click Okay and you should be good to go.
Your tileset can be individual tiles, however its much easier if you group your tiles onto one file. For example:
This tileset uses 16x16 tiles with 0 magins, and works just fine in Tiled.