It's not only you. I found Sea Clear EXTREMELY hard to use and annoying. I switched to OpenCPN (free) and Polar Navy (free for planning). I use Polar Navy on board.
I've heard this so many times that I have to agree that it's true. But that has not been my experience at all. Either I've stumbled onto the magic secret, or I don't make use of the features that are causing difficulty.
The one absolute rule of SeaClear is that you must run the separate MapCal program any time you add more charts. The first time you do this, you need to copy/paste in the pathname of the charts if you don't use SeaClear's default location (I tell SeaClear to look in the same folder as OpenCPN so that they share the same charts). Then you need to have it scan the directory so it can build its database. From then on, you don't need to worry about MapCal unless you add more charts.
The benefit of SeaClear is the ease with which you can move from one chart to another. So if you're planning a long cruise that takes you across multiple charts, it's so easy and quick to change charts just by double-clicking on the margin of the chart that's showing. Then other features like "Best Chart" to get the highest resolution, or "Smaller Scale" to get a lower resolution that covers more area. I also like the route editor for creating routes, and I use G7toWin to translate their route file format to .gpx to transfer into my Oregon 400c and/or OpenCPN.
But I do not use SeaClear for anything other than this, so maybe that's why my experience is better.
OpenCPN does a lot of things better for en route usage, such as course up (instead of north up) and quilting. But it's a little slower to change from one chart to the other, which is the prime reason I don't use it at home for planning. It also has a very nice display of AIS targets, with nice ability to customize the display and alarms.
I tried PolarNavy once and found the interface very non-intuitive. Maybe if I stuck to it I would have learned.