Steps to constrain a design

TimeQuest analyzes all edges, but a register only works on one edge. So if your register clocks data on the rising edge, TimeQuest only analyzes rising edges for that. If it clocks on the falling edge, it only analyzes falling edge transfers. Might I suggest looking at Section 2 of the following User Guide I put together:

http://www.alterawiki.com/wiki/timequest_user_guide

I generally find the most difficult part with hold time is that the default hold relationship follows the setup relationship, so if you add a multicycle -setup, the default hold relationship changes. That's usually the biggest stumbling block.