One of my favorite quotes is "With an Auto you steer, with a manual, you drive".
Stock for stock the manual, if shifted right, is usually a few tenths quicker than the automatic in the 1/4. This is usually due to the weight difference and gearing ratios of the tranny.
Yes I know with high hp drag cars an Auto is more consistant and such with different stall converters and shift kits, but unless you get into that professionally, stick with the stick.
Practice for a while and you will get better, trust me, it sounds like you just need to get used to the the capabilities...