OK here is the thing, when you install PHP manually, you get two files intact, production and development, if you are just using the PHP for developing site, you can safely rename the php-development.ini to php.ini and make changes to it as, same if for production.
when you install through WebPI, windows installer will automatically create php.ini file and then ADDS to its base, recommended settings. like for example, you'll find max_upload_limit= 4M in the php file, while when doing manually, you are commenting OUT those settings and extensions that you need, what windows installer do is, rather than commenting out the required extensions, it just adds to the base, so if you have configuration file already, then you'll find them typed in the base of that file and above that, will be exactly same as you'll find in either php-development/php-production file.
In that configuration file, at the bottom, you'll find information written like
[WebPIChanges]
error_log=C:\Windows\temp\PHP54_errors.log
upload_tmp_dir=C:\Windows\temp
etc etc
This above is the information added by WebPI to that configuration file, with its own configurations. all above that text will be as same as found in php-production.ini file.
for intl extension, all you have to do is, download intl extension.dll file, and then mention in your configuration file, restart IIS and you are good to go.
and yes UTF8 encoding is required.
Although WebPI does the jobs automatically, but I have always preferred doing it manually even in presence of wonderful WebPI option, if you want to take manual path, that can be assisted as well. As there is 64-bit PHP available for Windows Platform as well, whilst WebPI wont give option of that.