I've been playing for a few months now, and feel like I've sort of gotten into a bit of a rut as far as progressing goes. I've been lately working on combining different pentatonic shapes, but always seem to confuse myself a bit when moving between the boxes that I learned. However, I realized today that the boxes are just fragments of the scales as they appear up on string, and started thinking of the scales like this instead of as boxes...I found that because I have a pretty good knowledge of the fretboard, I can combine bits from the the same scales on different strings rather then from a box approach. I guess I'm just approaching it from a different way. Anyways, my question is, will this hurt my progress at all, or could it be bad in any way? I was really sort of proud of myself when I realized this, and could only seeing it helping (especially in my ability to see notes and music on the fretboard as opposed to a bunch of seemingly random boxes).
Thanks for any help or comments
getting out of boxes= great thing, not bad!

i fuse mode positions together to play up and down the neck.

try reading the 'hopscotch method' lessons in the UG lessons section.
Youtube covers

the way i origionally learned is a lot like the say your thinking now. put logically, a scale is a series of notes played in sequence with each other, so playing 10 nothes on the E string and playing 2 on each string are equal to the same thing. the way i saw scales was in terms of the entire fretboard. i actually hadnt even heard about "boxes" until like a year ago. i think this helped me a lot because it just comes natural to me to use the entire fretboard without thinking twice about it. it would be horribly boring for me to stay in one "box" or position on a scale.