The way I'm planning on doing it in my office I'm still remodeling is tear my carpet up, put down a layer of rigid foam insulation (prevent heat loss downward and use to adjust to optimum floor height), then wooden spacers for the pex tubing, lay pex tubing in grooves with aluminum heat spreaders (
example) as shown below.
Then, you just put your flooring on top of that. In my case I'm going with bamboo. This adds very a minimal amount of thickness to the floor.