- To manually add tilesets which are not the basic ones directly included in NeoLemmix (Graphic Sets tab)
I don't see what's the sense of this, since I've been noticing here many people making their levels with the same graphics.
Unless you're telling me not to make the same...levels?
To play a level pack, you need two files: The NeoLemmix player "NeoLemmix.exe" and the level pack file "YourPackName.nxp". This gives us three possible positions where to store graphics: The player itself, your level pack file or in an external style file in a subdirectory.
Graphic styles stored in the player: These are the original L1, ONML and christmas lemmings styles and most of namida's own graphic styles. You can freely use them and forget worrying about them when putting the pack together in the Flexi Toolkit.
Graphic styles in your level pack: For all other graphics it is recommended that you include them in your level pack file, which is what IchoTolot meant with his comment. Such graphics include the L2 (Tribes) styles or third party styles like GigaLem's, Gronkling's or IchoTolot's graphic styles.
Graphic styles in a subdirectory: This is mainly intended as a fail-safe to ensure that level packs are still playable, if a pack creator forgot to add them internally. This method to load graphics is used as well, when you play single levels, that are not part of a level pack.
All of this requires that your sprites (of single terrain pieces and objects, not of the whole level) are contained in a graphics style. So if you wish to use some graphics you made yourself and noone here has ever seen, then you will have to do an extra intermediate step to create the graphics style. Feel free to ask for further help, if you need this.
Summary: Use whatever graphics you want and whatever fits your level idea best, regardless of any issues with using the FlexiToolkit. We are looking forward to see your levels

. If you include your graphic styles in your pack, then even better. Only if you add graphics you made yourself, you have to be very careful.