My question concerns panel boards where the main breaker takes up two or three positions on the panel board. If I use a main in position 2,4,6 the corresponding positions 1,3,5 have to be left blank according to code.

No, the pole space opposite the main can be used for branch circuits, however the main breaker must be held in with a Main Breaker Retainer Kit, as per NEC 2002 edition, Section 408.16 (F) " plug in type devices that are backfed for supply ungrounded conductors shall be secured in place by an additional fastener that requires other than a pull to release the device from the mounting means on the panel"

Unless of course the breaker extends into that space, which most do not do any longer.

The retaining kit is different for each brand of circuit breaker/panel. Check with your breaker/panel supplier for the retainer kit.

Ands be sure to use the label that comes with the panel to mark the main breaker as "MAIN".

Thank you very much