suPHP vs. DSO (mod_php)

Hi,
I have several multisites. I have encountered permission errors lately and my server host suggests that I move to suPHP. They say I will no longer be able to use .htaccess. I will be using php.ini instead.

This is a little above my pay grade and concerns me. All plugin instructions and support forums I have ever seen only show modifications to .htaccess.

Will this be a simple move or something major that could break things and limit my access to WP plugins? (The host says they will help.)

I'm running WP 3.5.1, multisite, multi-DB on a VPS.

Thanks!
Chuck S.