Yes, both are MS-DOS programs. Not all MS-DOS applications are made alike. SNEStool has its own menuing system programmed into it. inSNESt requires command line parameters to function.
For example, if you wanted to split a ROM using inSNESt, open Start -> Run and type "C:\insnest\insnest.exe s rom.smc" (no quotes) and you will be presented with a menu of options to split the ROM.
Here is a complete list of inSNESt's command line options:
Usage : inSNESt i : View internal ROM information
c : Convert to specific copier type
s : Split file interactively
j : Join previously split image
r : Rename internal ROM Name
p : Attempt NTSC to PAL fix
n : Attempt PAL to NTSC fix
f : Slow ROM�protection fix
v : Apply PSF2 Save RAM fix
m : Save RAM protection fix
h : Checksum/CRC Repair fix
a : Affix IPS Patch to ROM
l : Create Listing of SNES ROMs
o : Pad ROM to valid Megabit size
? : inSNESt Help System
e : Credits and Resources