Jerky gears on a yamaha YBR 125cc?

I've only been riding since february but and I'm improving all the time ( says my mate who rides a GSXR 1100!) but one thing that keeps irking me is that its jerking through 1st and 2nd. I've tried different ways like giving it more trottle (bad idea...s-h-i-t meself!) to changing up and almost coasting before going up to 3,4 and 5 which always change up and down smooth as yer like. is this down to me being a newbie or is it just 'one of those things'? One more question- would a 125 cope with a 250 mile journey. obviously i'll be stopping for rests! thanks