Whether or not you should use a pilot as both remote and organiser depends on your personal circumstances.
You can use it as both if the following are true

1. You are single or noone else is likely to use your home icnema set-up whilst you are away - therefore it doesn't matter if the pilot is not in situ.

2. Anyone else in the household who uses the pilot as a remote is proficient in using the original remotes if the pilot is not available - the home cinema set-up is still usable if the pilot is not in situ.

Consider with care using the pilot as your main remote if the following is true.

1. You have a wife / girlfriend / partner / kids who want to use your home cinema set-up but would be absolutely stranded if you took away the nice friendly macros that do everything for them - no pilot means no home cinema for these people.

2. You have a wife/ girlfriend / partner / kids who likes to fiddle with your pilot and accidentrally delete all that important information (calendars / appointments / phone numbers) you haven't had a chance to back up yet - boy are you going to be pissed by the sheepish looks on their faces as they hand you a pilot with the black screen of death.