ACF is great for a few maps and a few markers, but for something like what you’re talking about you may need to go a different route. Not that ACF isn’t great, but all plugins have their limits. We recently built a site for a client that required maps with several thousand markers on it. I used http://www.wpgmaps.com/ and purchased the developer bundle. The map we created for them uses a local .kmz file to hold the data.