As long as you can use the in-game waypoint editor and a text editor you can waypoint. Some waypointers bind a key to add a node AND then autoconnect (so hobbit's autoconnect button isn't really needed). Where Hobbits tool excels is verification and reading the bsp (needed if you get into custom script files) Ent numbers can normally be figured out by /viewent or /configstrings.
I'll try downloading from his webpage again JIC he made a recent change or there is a download problem.
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Hobbits tool only reads unpacked files so did you only unpack or create 2 navs?
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the latest downloaded copy has a md5 of
2A6603CDDC3088ECF3B9F5E241C1D12A
on the zip file, And runs fine as far as I can tell.