In many clubs/groups the policy seem to be that as soon as you can ride a bike you should switch to being clipped in as it is so much better for you. It is one of the questions debated on the mountain biking chat forums on a regular basis: flat pedals versus SPD (clipless pedals). In my opinion it is very simple, get a good pair of big flat pedals with grippy shoes (not SPD shoes!) and first learn to ride so well that you very rarely have to put your foot down, then decide whether you would like to try SPDs or not. Personally I have SPD on my road bike but never found the need to be clipped in on a mountain bike where I much prefer the flexibility of flat pedals.
By learning to ride using flat pedals you will relax more and relaxing more makes you ride better. Being clipped in while still being nervous about technical riding will make your riding worse as you will be tense, but the consequence of this is masked by the fact that you are artificially stuck to your pedals so you won't bounce off them. With flat pedals on the other hand you HAVE TO be more relaxed as otherwise you risk bouncing off. Once you feel that you ride well enough to relax (or relax well enough to ride well!!) try using SPDs if you like the idea of getting slightly better pedalling efficiency. But don't get lazy! And don't forget how to ride your bike and not just be a passenger! And if you don't like the SPDs don't persevere with them for more than a couple of months and just invest in a pair of nice flat pedals and grippy shoes and have fun!
So for the courses then? Which pedals to use? If you normally ride using SPDs and you are not a nervous rider then stick to the SPDs. If you are using flat pedals then don't change to SPDs for the course it will not benefit you in any way. If you very recently have switched to SPDs or tend to unclip for obstacles when you are out riding because you get nervous then I would recommend using your flat pedals for the course.