Bill,
Tide information is used by subtracting the tide height at a given point in time from the recorded depth of each track-point. This should effectively give you the low water height for each position, contingent of course on the tide data being accurate. If you are using data from wxtide32 I would advise checking the data over a range of times to assess how accurate it is - it can be better in some areas than others. If it's not so good, then you should use your own data - I find entering a couple of points by hand for each recorded track is the easiest way to go.
It is easy to combine waypoints - just put the mouse into "region select" mode and draw a box around the waypoints you want in a set. Then choose either "move to" or "copy to", and choose a destination set. The destination set can be an existing set, or you can create a new one. Any selected waypoints that are already in the selected destination set will not be re-copied. You can also ahieve the same thing by selecting waypoints in the waypoint list (Waypoints tab of the Global View). You can sort waypoints by various attributes in the list (e.g. date, latitude or longitude), which can be useful, although you can only view one set at a time in the list.
Matt