Yes. When there is more than one radical, you first need to identify the primary radical. The primary radical is determined by its placement: (1) top, (2) left, (3) bottom, (4) right.
examples:
薬
"Grass" (kangxi #140) on top. "Tree" (kangxi #75) on bottom. So, two radicals, but you use the grass radical to look it up in a dictionary.
好
"Female" (kangxi #38) on left. "Child" (kangxi #39) on right. So, "female" is reference radical, but there still are two radicals.
薄
"Grass" (kangxi #140) radical on top. "Water" (kangxi #85) radical to left. Kangxi #41 (the "Sun"?) radical on bottom. So, the top radical is most important. The reference radical is "grass".
Organizing kanji is already difficult enough. Making a kanji such as 薄 referenceable by all 3 radicals would just be untenable. The (top / left / bottom / right) rule solves that problem.
Also, the number of strokes in a radical enhances its precedence... yes. it can be very frustrating using kanji dictionaries such as Nelson. People these days just use handwriting recognition. For example, one dark day I was brought to tears looking for "音". I kept referencing by the smaller radicals I saw. But in fact the whole kanji is a radical by itself. You've got my respect for using dictionaries instead of handwriting recognition!