Hitting and receiving damage counts as the usual method of doing an 'exp tap.' However, with homunculi, it's a bit different. If you strike a monster and do 1 damage, or take damage from the monster, while your homunculus is hitting or taking damage from the monster, and you both survive by the time it is dead, the monster would of been considered 'tapped' once, which is 125% the usual exp.
As usual, you would receive 125% of the base exp, and your homun would receive exp in proportion to how much damage it did to the monster out of that 125% pool, on the drawback that you will receive only the amount of job exp in proportion to the damage you done.
To maximize the experience your homun receives, the best way would be to hit a monster once, and do as little damage as possible, just so the monster will be tapped for the 125% exp, then let your homun do the rest.. The bad side is that you'd only receive about 1-50 job exp per kill depending on the monster.
In the end, if you use a homun for all of your training after you are able, your homun will hit 99 while you are level 93~97 depending on whether you do a lot of damage to a monster or minimal damage, as you will still progress at the same rate in terms of base exp regardless of the method, but the homunculus will not.
In terms of intimacy, if you train it at places like zenorcs, your homun will most likely hit loyal before 99, however, if you train at higher exp places like Niff after your homun is strong enough, your homun will hit 99 days or even weeks before loyal, assuming you never starve it and don't idle around in town just to get homun intimacy up.
Finally... Despite some answers on the forums, your homunculus' intimacy will /not/ reset in any way if you or the homun dies. i.e. If your homun was one point from loyal, and it died, it will still be only one point from loyal after you res it. The only way to lower your homun's intimacy is to starve it, overfeed it, or use the 'extreme' skills such as Self-Destruct and S.B.R.44.
EDIT: Tested it a while ago while my homun was only gaining 0.4% per kill on it's own, when I struck the monster once and left it alone for the homun to kill it, it received 0.6%, and followed that pattern so it couldn't have simply been a decimal rounding off.
