First, your footage interpretation must be correct. If it was shot at 25 it must be interpreted at 25. Do Not change the frame rate to match the composition. The only reason to change the frame rate of any footage from the as shot frame rate is to change the speed of the playback.
If you have 60i footage and you want to convert the footage to 25p then you must accept the fact that you are going to be combining frames. AE does a fine job of this going from 60 (really 59.94) to lower frame rates but 3rd party solutions like Twixtor do a better job. The add 3:2 pull down and interlace the footage is a way to go from a 29.97 comp to a 23.976 fps playback to create a telecine look from video, but there is no formula to go from 60i or 60p to 25 without loosing any frame data, so just make sure you have your final comp set to the frame rate you wish to use for delivery (should be 24, 25, 23.976, 29.97 or 30 in almost every case) and make sure the footage is interpreted as shot.
If I understand you correctly, you advice me to convert those 60p clips (in Twixtor pro ) before importing them into my 25p project ?
You may not need to. Put the 60P clips in a 25fps comp and render a test or step through the comp one frame at a time and see how things look. Frame blending on and frame blending off. The conversion may be a waste of time. There is a caveat.
If you are doing a bunch of manipulation with the 60p footage like roto, keying, camera tracking, then do all of that before you incorporate the footage in your 25fps comp. The workflow depends on the project, but generally, all heavy manipulation of video should be done at the native frame rate and if the footage is interlaced the fields should be separated so you are working with as much original data as you can. You then assemble the comp for final rendering. Run some test to determine whether or not the shot benefits from using Twixtor.