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If you use 1- or 2-star alignment you should pick your alignment stars on the same side of the meridian as the the objects you want to observe. Since you will have no cone error correction pointing accuracy can be reduced after a meridian flip.
Alignment stars should preferably have low declination (be close to the equator) in order to maximise resolution in RA. They should be between 3 and 9 hours apart in RA and between 10 and 30 degrees apart in declination.
Section 3.7 of the SynScan manual (v.3.35) explains the rules for choosing alignment stars.
Cheers
Steffen.
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