Q: safe torrent app that will work with El Capitan,

uTorrent for OS X is bundled with adware.  OS X El Capitan has System Integrity Protection to protect again adware and malware.  About System Integrity Protection on your Mac - Apple Support

If you absolutely need a torrent client to download something legal such as a Linux distro, try qBittorrent which is open source.  If you're having issues with iCloud or iBooks provide us some details or screenshots with what is happening.

Stuuty wrote:

 

since upgrading to el capitan, my U torrent will not work, I cannot get into iCloud, and my e books, that were on iTunes and supposed to have been transferred to e book have disappeared...not happy Jan

I'd say about 95% of the time, torrent clients are used for illegally acquiring copyrighted material.  We can help you with your iBooks/iCloud problems, but if you need a torrent client that bad, you should Google it.  I know there are legitimate uses for torrent clients, but no one here can know what your intentions are for such a piece of software because hey, it's the Internet — you can easily lie. 

FWIW, Transmission is the best Torrent client for OSX despite the fact they were hacked recently.

Dialabrains assessment is indeed the case.

Transmission is the one not intentionally bundled with cr@pware by the distributor, but they did have their @$$e$ hacked and a securities Lab in Palo Alto had to tell them because they were clueless to that fact.

but if you are not using any torrent client to obtain the apparently smaller assortment of legally distributed software then the integrity of your torrent app choice will be the least of your worries.

If you absolutely have a need for a torrent client, make sure that you download them from the develpper's wbaite, rather than some third-party distributor.

Otherwise, I second dialabrain and chroot  recommendatins.