The analysis of the structure of musical pieces is a task that remains a challenge for Artificial Intelligence, especially in the field of Deep Learning. It requires prior identification of structural boundaries of the music pieces. This structural boundary analysis has recently been studied with unsupervised methods and \textit{end-to-end} techniques such as Convolutional Neural Networks (CNN) using Mel-Scaled Log-magnitude Spectograms features (MLS), Self-Similarity Matrices (SSM) or Self-Similarity Lag Matrices (SSLM) as inputs and trained with human annotations. Several studies have been published divided into unsupervised and \textit{end-to-end} methods in which pre-processing is done in different ways, using different distance metrics and audio characteristics, so a generalized pre-processing method to compute model inputs is missing. The objective of this work is to establish a general method of pre-processing these inputs by comparing the inputs calculated from different pooling strategies, distance metrics and audio characteristics, also taking into account the computing time to obtain them. We also establish the most effective combination of inputs to be delivered to the CNN in order to establish the most efficient way to extract the limits of the structure of the music pieces. With an adequate combination of input matrices and pooling strategies we obtain a measurement accuracy $F_1$ of 0.411 that outperforms the current one obtained under the same conditions.