Try reading the tips given in the FAQ under “Backup jobs are running forever!”
It’s the solution to this problem, too.
https://www.ads-software.com/plugins/backwpup/faq/
FYI: The problem isn’t the plugin, it’s in how the server you have your site hosted on is configured. That is what is causing all the issues.
I have used this plugin on both large and small sites, and on some servers, large sites upload just fine, and on others they don’t.
I have even had issues on some servers with small sites, where the site needed to be split up as suggested in the FAQ to keep the backup file sizes under 5mb.
You need to find out what the upload limitations are for the server that is hosting your site and then figure out a way to split it up to stay under that size limit.
There is no way for any of us to know what the limits are on your server. That’s something you’d have to ask your web host.