If you travel or go around places a lot by cars, bus, or train (not plane cause you can't use wifi), bring your 3DS and don't shut it down. Pretty sure you know this, but StreetPass will help you grab people with a copy of the game. Find all their bases first, so bring along both bikes , all HMs, and etc. Next, use your AreaNav and click on the map. (Basic Stuff, if you don't need this part just skip ahead.) Select bases. All the areas with shaded squares means you've found all secret bases on that route. White squares indicate that there are some bases you haven't found. Look for bases everyday. Their flag regenerates everyday. Add some secret pals; some of them give you flags if you talk to them. I got 5 flags from this pal once :D
Hoped this helped, kind of long, sorry :( Most of this is basic so you should kind of know.