Ok, you are certainly bouncing from topic to topic, so it is making it difficult to track.
for your question about the tiles not showing up, you will notice that EVERY tile has a section similar to this:
TopLeft=Forest
TopLeftHeight=0
TopRight=Forest
TopRightHeight=0
etc... for all top and bottom corners of each tile.
Those lines are referring to the terrain type of the tile(s) they will paint next to. They will ONLY pain when all four corners match their individual description. So, in this case, for the first tile, you MUST have a section of ground that has Forest tiles in a 3x3 grid to get that particular tile to paint.
Below those you will have:
Top=
Right=
Bottom=
Left=
Those are for crossers... say fences, streams etc. If they are blank, then the tiles next to your new tile must also not have a crosser in that location. So a tile to the right may NOT have a road connecting to it's left edge, a tile on the TOP may NOT have a road on the bottom edge etc...
so basically you have to match terrains AND crossers for any tile to paint.
If a tile-set is completely setup correctly, the engine can auto-select matching tiles and paint them for you providing the matching terrains and tiles exist.
Now if you mean that you can not choose a given tile from the menus on the right, those are controlled by the 2 different itp files. You only require 2 itp files if you have changed the base layout.
IE, base for tiles is:
Features
Groups
Terrains
Where features has a single column of single tiles
groups has a list of various groups of 1x2, 2x2, 3x3 etc groups
and Terrains has all your base terrains like grass, forest, water, etc AND your various crossers like roads and streams.
If you want to change that list, IE add something other than Features, say call it "My Forest Features" and have a separate section might be "My Grass Features" etc, then you would have to generate a 2nd itp file to handle that.
Typically, the main ITP file that you edit is called "tilesetpalstd.itp" and if you have created extra headings, you would also have a "tilesetpal.itp
Basically the tilesetpalSTD.ITP is the one that has the most entries as it lists everything, all features, groups, terrains, crossers etc.
Changes to the standard pallette are handled in the tilesetpal.itp. If you look at sizes, you can easily see that the palSTD file is almost always larger as it has more entries in it.
I normally just use TLKedit.exe, but I don't have a link for it, sorry. That one has always served me very well in editing the various talk tables AND pallette files as needed. Note that since the pallette files, the ITP do utilize the actual tlk table file, you will end up learning a bit about that talk table as well. Of course the tlk table is just a basic 2ds type file where it lists a number and the associated line of text. The Pallette files related to the line number in the tlk table to grab the name to display, ie, say "forest" is line number 239 then the entry in the itp will reference that line number. (note, that is NOT the correct number, I am just using it for an example)
NOTE: One thing I would double check, you say you added the new tiles... I assume you also adjusted the total tile count near the top of the .SET file? If that is not correct, IE if you added 2 tiles and now have 102 total tiles in the hak, but the .SET file still says it only has 100 tiles, then your new tiles will also not work, AND you may have problems with getting the groups to work as well. Same goes for groups, if you add new groups, you MUST edit the group count in the .SET file also. This is a very easy mistake to miss when adding stuff to a tile-set.