generally, the main differences in cooking are that it takes less time and some things can dry out a bit. however, you do have to be careful of hot spots, and in my experience this is a quirky issue. no two ovens seem to be the same. you might expect that the area directly hit by the fan to be the hottest and fastest cooking, but i find that hot spots can develop here and there, depending on the size, shape & number of pans.
convection ovens here in japan have the fans on all the time, but professional ovens i've used in the past usually had a switch to have the fan either on or off. if you have no control over the fan, try to keep your loaves centered in the oven with as much space between the loaves themselves and the walls, top & bottom of the oven to allow for better circulation. the only other lame advice i can think of is, try to place the pans a little bit further away from the areas where you've observed the hot spots to be.
you can use a baking sheet for bagguettes, etc. but the large sheet will further reduce or at least complicate the air circulation pattern. so if you were to place a regular loaf pan on top of a baking sheet, most likely either other hot spots would develop or not enough heat would reach that area of the oven. but, there's also a chance it could work out great. the only way to find out it to experiment.
best of luck