I would recommend that you configure the software RAID-1 when you install the server. It is much easier and less trouble prone than trying to create it after the fact. Also this will ensure that mdadm gets built into your ram image for support from the start. This will add a small amount of complexity to the partitioning process. I use this very same technique on one of my servers to provide mirroring of the HD and from what I can tell, it works very well. Based upon your usage description, I don't think you will have any problems. You are clearly not in what would typically be considered a "production" use case. I would also recommend that you just go ahead and put the entire system on the hard drive and forget the compact flash cards for two reasons. First, hard drives are very reliable and don't suffer from write/erase limitations which can be problematic for flash as as OS because the same sectors will tend to get hit a lot. Second, if you mirror your drives and make them both bootable, you will be able to fully boot and run your system with only one drive should you need.
When you perform the install, you will need to partition your drives. I don't recall the exact process, but when you do this, select that you want to make a raid partition. It will then ask you which devices to add to the raid and the type of raid you want. The process is quite straight forward, but you may need to do a little trial and error.From there you can create the various partitions for your server. You may want to make separate root and home partitions but this really doesn't matter. You should create a swap partition though. When I created mine, I made a small swap partition at the top of both drives (they are identical mirrors). The easiest way to go is to make one large raid 1 partition, mount it as /. Unless you plan to install multiple distributions or something this will be fine.