Leveling up skill levels of SR weapons you will use for a long time is a better option to start off with. You don't need to max them right away but getting their skill level to somewhere decent. SSRs may have a higher base value but all weapon skills increase the same amount, that being 0.5% per level but SR weapons require less to level up skill, making it more easier to level for the same amount of boost. When it starts getting difficult to skill level the SR, then move onto the SSRs then you can start alternating between each or max whatever you want.