Hi Lucie,
I had exactly the same problem with dd when she had very bad eczema and impetigo as a baby. Have you tasted Fluclox? It truly is disgusting, so my sympathies are with our poor children, having to take the stuff!
Unfortunately it is the best stuff to give for skin infections - I asked them for an alternative, was given something else (can't remember what) but as soon as the course finished, the problem came back. The fluclox is the only stuff that does the trick, goddammit! Hopefully someone out there will have had good experiences of alternative remedies, but I've not tried any.
My OH is utterly soft and useless with any kind of medicine giving (won't even give a pill to the cats) so it was entirely down to me to do it.
How old is your ds? DD was 15 months. What worked for me (although there were a few episodes of pinning down and flailing limbs which, yes, do make you feel like the shittest mother on the planet), was using one of the orange plastic syringes that they supply with the baby nurofen liquid - dunno why, but they just seem easier to empty - then, putting it in the side of her mouth, at the back of the teeth, and shoving the plunger down all in one go.
In my pre-dd life, I had to worm horses on a regular basis and, scarily, the same tactic of putting your little finger into the corner of the mouth and (very gently, for a LO!) pulling it down to be able to insert the syringe works quite well! I tended to do this while holding her in my arms in a 'rockabye' position (if that makes sense?) as I got better leverage...
The whole time I was doing it I was telling her it was medicine to make her better and if she didn't take it she wouldn't get better, which she did appear to take in - but then dd is/was fairly eager to please when she's not poorly, so not sure if that would have any effect on your ds!
Anyway, I do feel for you, it's horrible to have to force medicine on a child - if it helps, it doesn't seem to have traumatised dd at all - she happily gulped down some Medised for her chicken pox just now before nap time!