As a qualified nurse and acupuncturist who is also recovering from a whiplash injury, I can come at this problem from more than one angle! You have my sympathies, as I am finding that this is not an easy condition to treat or live with.
Firstly, there are many in fields as diverse as neurosurgery, osteopathy, counselling, acupuncture...who believe strongly that physiotherapy is counter-productive and should be avoided, particularly in the early/acute phases of whiplash: this is sometimes said of osteopathy or chiropractic, too. It's felt that the usual techniques are likley to irritate already hypersensitive tissues, thereby aggravating and prolonging response to stimulii, which is the major problem in whiplash. Provided you have been checked out for bony injury (you should by now have had at least an Xray, and hopefully an fMRI scan to exclude this) the best course of acton is regular, gentle treatments that aim to reduce sensitivity and relax the nerve/muscle spasm that creates so many problems.
As an acupuncturist my area of expertise is in fertility/maternity/postnatal/gynae, so I rarely treat patients with whiplash or similar injuries. However, my regular acupuncturist is well-versed in the treatment. So, make sure your practitioner has plenty of experience, and has at least one modality available to them - that is, do they practice TCM and 5-element, or just the one? Can they prescribe herbs; do they do tuina or shiatsu? Some people set up as acupuncturists with only a rudimentary training therefore cannot diagnose and treat complex cases. Any proper acupuncturist will not be offended at your asking them about their expertise and qualifications, nor mind suggesting suitably experienced people to you. After all, it's YOUR interests we are concerned with. I have found that gentle work on SI, TH and GB makes a difference, albeit over a series of weeks, and at regular two week intervals. Also, I am prescribed Xiao Yao Wan (herb) to help relax the muscles. Giovanni Maciocia has extensive suggestions re: treatment but, within the context of a proper diagnosis. Again, your chosen practitioner should know who he is!
Secondly, have you considered cranial osteopathy? This is very very gentle, and is excellent at releasing embodied tension in a non-traumatic way. It is commonly used for newborns who have had traumatic deliveries so, if it's gentle enough for a baby, it's gentle enough for you!
Third, do some simple re-framing exercises (psychologically speaking). I have found it very dispiriting, frustrating and almost depressing if I experience a relapse, and learning to view the days when I can't function as beneficial is a work in progress - but getting there!
I hope you are being monitored by your insurance company and a solicitor in all this. You need to afford the best treatment possible, as whiplash is notorious for causing long-term damage if not cared for in good time. I agree that treatment should not make things worse, although sometimes fatigue or weariness is normal for 12 hours or so after. The effort of holding your head up on a poorly neck and shoulders can be exhausting and, when relieved, the relaxation effect is quite powerful. But, that's a good after-effect. Your physical symptoms should not be heightened.
Good luck! I do, really, know how you feel ;-)