as above, specifics help and wait for advice based on pics (and from better fetters than me) but in general: remove the rust - I get on best with wet or dry sandpaper or wire wool, taking the corroded surface back to good metal and expose a small area of clean good metal around it so you know you've cleared the problem before covering it up again, carefully fill any pits in the metal - car body filler o.n.o and smooth it off to a smooth even surface then prime, paint and lacquer.
Touch up pens are ok if the bike is a fairly standard colour - and beware of drips and over filling the brush/nib and the paint running. If you want to be absolutely precise colour wise, you'd need to go to a specific (auto) paint outlet with the bike where they will be able to colour match to the rest & blend a small pot to your requirements. more costly and you'll end up with plenty of spare paint but its down to your personal preference and if the bike is pride and joy & wanted as showroom condition or to be used and will get knocked and dinged in the course of its working life.
For some people near enough is good enough, for some, it has to be an invisible join.