It sounds like you got some dirty dope.. Your dope should pull right through your cotton and really you shouldn't have anything left beh ind. The poitn of cotton is to catch larger particles.. but if your cotton is getting 'clogged' chances are you have a lot of insoluable cuts. The few times I ahve gotten shitty or fake dope it was a chore to get it in the pin. The good shit pulls through easy and clean doesn't chang ethe color of cotton at all.
IMO a micron is not necessary if you get decent dope.. pills on the other hand it's vital. Will it hurt you? Hell no. If you can afford the micron's buy them by all means./
Also are you using a whole q-tip? All you need is to tear a litlt epiece off and ball it up, like size of a marijuana seedc.