You won't experience any issues. Have yet to see any arise that didn't have a quick and easy fix. (Permissions usually)
Here is the long and short of it

Thanks to Katrina for producing most of this:
--
Your server has changed to suPHP as a security upgrade. If you are
running a PHP-based script on your site and are receiving
a 500 and/or 404 errors on your pages, it is likely you have one or more of
the following occurring:
1. The permissions on some of the folders or files are 777 or 666. If this
is the case, change them to either 755 or 644 in Cpanel's File Manager (or
using your local FTP client).
2. The files and/or folders are not owned by you. Certain applications
having been run under php as an apache module may have files owned by the
apache user of nobody. An indication that you don't own the files would be
if you are unable to change their file permissions. To correct this, please
provide your username and the last 4 digits of your credit card on file with
us for ownership verification (no charges apply) and provide the location of
the folder or files that need to have your ownership.
3. Your .htaccess file has php_values or php_flags in it. This causes a 500
Internal server error when attempting to execute the script.
The php_values and php_flags will need to be removed from your .htaccess file
(please make a backup of the .htaccess by copying its contents and saving it
on your desktop as htaccess.txt). Take the contents removed from .htaccess
and place it into a file you create called php.ini. Remember to remove the
php_flag and php_value part before the directives as php.ini files do not
require those in front of the values. You can always make the changes and
ask us if the changed files are correct.
Because php.ini values are not shared across directories, you would need a
separate php.ini file in each folder that has .htaccess or that requires the
php_values or php_flags. In order to avoid doing this, you can place a line
in the .htaccess file in your public_html folder to have all values in your
public_html php.ini to be shared across all folder. This line would be the
following:
suPHP_ConfigPath /home/username/public_html
Finally, to explain in depth why suPHP requires these changes to the file
permissions, please note that suPHP runs scripts with the permissions of
their owners. Regular PHP executes scripts under the permissions of the
system user running the web server, which means that your script runs with
different permissions than your own user account and makes it very hard to
use a PHP script to modify and create files without giving everyone on the
server access to your files (this means that on regular PHP you provide write
or execute access to group and world even for some files). Since SuPHP makes
your PHP scripts run with the same permissions as your regular user account,
you do not need group or world write access or execute access for files and
suPHP will even prevent files from running that are group or world writable
or executable as a security precaution.
666 equals the following:
Code:
Mode User Group World
Read 4 4 4 (all checked)
Write 2 2 2 (all checked)
Execute(none checked)
This makes group and world able to write to the file, a security risk
777 equals the following:
Code:
Mode User Group World
Read 4 4 4 (all checked)
Write 2 2 2 (all checked)
Execute 1 1 1 (all checked)
This makes group and world able to write and execute the file, a very large
security risk.
Basically, suPHP is more secure, and preventing scripts from running as 666
or 777 prevents group or world from maliciously writing to the files and
hacking your scripts.
- Ed