A tricky point is equation labelling and numbering. tbook supports three ways of giving an equation a label:
<math> element has an id attribute. For example:
<math id="Einstein">
<mi>E</mi>
<mo>=</mo>
<mi>m</mi>
<msup>
<mi>c</mi>
<mn>2</mn>
</msup>
</math>
or simply
<dm id="Einstein">E=mc^2</dm>
You can refer to it with
<p>The <ref refid="Einstein">equation</ref> is the famous energy
equivalence.</p>
<mtd> element with an id within an equation
array:
<math>
<mtable groupalign="right center left">
<mtr>
<mtd id="equation1"> <m> 1+1 #=# 2 </m> </mtd>
<mtd> <m> 4 #=# 2 · 2 </m> </mtd>
</mtr>
</mtable>
</math>
which you can refer to by saying
<p>If you want to see a pretty useless equation have a look at
<ref refid="equation1">equation</ref>.</p>
<mlabeledtr> element with an id within an
equation array, and the contents of the first <mtd> element of
such an <mlabeledtr> row. This version is pretty obscure, and
you cannot refer to it with <ref> but only with
<mathref>.
I would recommend you to use only 1. and 2.