Clearing Check engine codes

My 2005 wrangler had vibration under the hood somewhere a week or so later
lost per and stalled. Took it advanced and 11 different codes came up. Had a
lot of work done in last 6 months and never cleared the old codes for the parts I
had fixed. Only new code I noticed was crankshaft position sensor, changed
that and 2nd days later vibration is back. How do I clear codes so when engine
light comes on I can take it and get correct code. Thanks in advance