oh sorry, of course, you're right again ;)
please take a look at the attached example. you can see a typical 16 steps loop is loaded into intrument 1. the loop is in 44.1 khz, mono, 16 bit. milkytracker automatically finetuned this sample to "-28" and adjusted the relative note to F-6 (+29). this makes C-4 the "base-note" or default note. that means you play the original loop in it's original speed/pitch (so to say) by entering a C-4 note. C-3 would half the pitch (making the loop play twice as long) while C-5 doubles the pitch (making the loop play twice as fast as a C-4 note)...
you can see that the sample-size for instument 1 is 1B6C0 in hex (roughly 220 kb). you can see this in the bottom right corner in the sample editor where it says "length". a tiny "h" is printed there. you can hit the "h" to cycle through hexadecimal, decimal and time display. but let's stick to hex in this case (make sure the "h" is visible).
leaving the size as it is won't allow you to use full-scale 9xx effects here (as descibed above). in order to use full-scale 9xx effects you need to "shrink" the sample-size to 64 kb (or 10000 in hex). the resampler (which is a native feature in milky ;) will do the job. simply right-click into the waveform, select "advanced" and "resampler..." and you're in the resampler dialog. now adjust the relative-note value (or any other) until the "new size" value is below 10000. something like FFDF or so. FFFF is hard to get but would be the optimal size. just try and see what you get and remember there's an undo button in the sample editor ;) hit OK and you're done.
ok, now back to the example loop. the loop's bpm is somewhere around 94. you can adjust the song's bpm value to 94 and notice that it is almost perfectly looping without further finetuning and all that. also try 188 bpm and 47 bpm (i did that for you in the example file).
while instument 1 is the original, unaltered sample, instument number 2 is the resampled one (FFDF). a 96E command on instument 1 would play the loop starting with the "snare". you can see that in the example pattern. the same 96E command played on instument 2 would start from somewhere near the second "drum" in the loop. so you cannot use the same 9XX commands for both instuments, because instrument 1's size is above the range of the 9XX command. a 9FF command (the maximum) on instument 1 will leave you somewhere 3/4 far in the loop while a 9FF on instument 2 is useless because the sample size is just below FFFF hex (10000 in decimal).
it is very important to do all the resampling and finetuning BEFORE you start entering 9XX commands.
now, with the resampled instument 2 you have full control over each of the 256 possible offset values (9XX). ok, i know 2 values are missing in this case ;) in reality you don't need to be that precise. normally you would just need to know which offset is the "kick", "snare" and "hihat" (depending on what kind of sample you want to use, but i'm talking about drum loops here).
this is a very simple example. the next step would be to adjust the pitch of the loop to your song. let's say your song is in 125 bpm and the loop is in 94 bpm. in this example your "base-note" would then be F-4 in order to make a smooth loop (more or less)...
you see it is acctually quite easy (but difficult to explain). when entering 9XX commands it is a good idea to have the sample editor open so that you can see which value triggers which offset in the sample. place your cursor on the note and use the ALT-SPACE shortcut (press and hold). once you release the keycombo you'll be thrown back to where you came from. once you got the "right" offset values it is just a matter of copy and paste...
"funktempo" is sometimes called "shuffle" in other (commercial) programs. it is not a feature but a trick that trackers sometimes use to create a dynamic shuffle rhythm. it is easily done by placing a couple of FXX commands on every row in the pattern like this: F07, F03, F07, F03, F07 and so on. this would produce some kind of reggae-style emphasis on every even row. if, for example, your loop plays just a little longer than 94 bpm, but too short for 95 bpm you could try 94.5 bpm using funktempo.