What are the differences between Zen and Taoist meditation? This is how I look at it:
In the briefest way to look at it, Zen meditation works with the Central Chi-channel (中脈 central nadi or Sushumna), and not necessarily work with chakras, but from my own experience, it is better to work with them in terms of chi-generation. A practitioner of Zazen (seated Zen meditation 坐禅) empties his mind and mindfully focuses on his central nadi. The benefit for a beginning meditator is that it is easier for him to "empty his body" this way. The weakness of going straightforwardly into the central nadi meditation is that for a novice, chi will usually be weak, therefore long-hours of meditation time is required before a meaningful amount of chi can be generated this way. Of course there is no problem for practitioners going for a few days Zen retreat where there is practically nothing else expected to be done! One can therefore clear up one's mind after the retreat and generally revitalized after a period of low-fat, low-salt vegetarian diet. Good for a practitioners' body and mind.
Again in the briefest way to look at things, Taoist meditation works with the Ren and Du Mai (任脈，督脈)，with chi primarily going up one's back side along the spinal cord. It is interesting to note that in the practice of tai-chi as chi-kung, chi is usually required to go up one's back instead of up one's spinal cord (Du Mai). In tai-chi lingo, it is called "chi nestles up one's back" (氣貼背). Fair to say those tai-chi practices closer to their Taoist origin still demand chi going up one's spinal cord. The pros and cons are just opposite to Zen's approach. Chi will be stronger because a practitioner is required to mindfully make his chi into a dense ball and make it go up his spinal cord. And because the practitioner will be busily minding these activities, oftentimes he will find it more difficult to empty this body for an empty mind. Unless you're only practicing moving tai-chi form, it is then not much of problem.
As the old saying goes, whichever route a practitioner begins, it all leads to the same destination. One will be required to have strong chi and able to empty one's body and mind, assuming that a practitioner aims at seeking a meaningful fusion of his body and mind. Or in Zen or Tao lingo: Achieving tao, tao with a small letter "t" (得道).