To give the second rule higher specificity you can always use parts of the first rule. In this case I would add table.rule1 tr
from rule one and add it to rule two.
table.rule1 tr td {
background-color: #ff0000;
}
table.rule1 tr td.rule2 {
background-color: #ffff00;
}
After a while I find this gets natural, but I know some people disagree. For those people I would suggest looking into LESS or SASS.