On the mechanics of calling fouls, the best advice ever given to me is to SLOW DOWN. At the time of the foul, hit your whistle, and then announce what you have in this order... who fouled, what kind of foul you have if it's not obvious, who the shooter is, and how many free throws (s)he'll have. I try to announce this loud enough that my partner, the table and both coaches can hear it. Taking 3-4 extra seconds to get all this straight is much preferable to losing a shooter or leaving your partner in the dark as to what you have.
Regarding the question about bonus situations, I try to use time-outs to check with the table on the current number of team fouls. This way, I'm usually aware of how close each team is getting to the seventh and tenth fouls. Echoing the message above, the scoreboard can also be used as a guide, depending on your confidence in the overall reliability of the scoreboard operator.
Good luck!
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