I dont quite understand the word order in this sentence, if anyone could help? thank you 
I’m not native Dutch, but I’ll give a stab at this.
Insert a comma between the phrase that ends in moet praten and the phrase that begins with moet and it may become clearer for you. Just like in English, ‘dan’ (like ‘then’) is often implied but not spoken. In the second phrase, ‘maar’ — besides carrying the meaning of ‘just’ or ‘only’ — also softens ‘moet,’ so that it is a polite request, not a demand. Much the same can be said for ‘wat’ in the first phrase, it softens the expression:
Als ik wat langzamer moet praten, (dan) moet je het maar zeggen.
If I somewhat slower need to talk, (then) need you it only to say.
If you need me to talk a bit slower, just let me know.
If, on the other hand, you said, “Als ik langzamer moet praten, moet je het zeggen,” that would sound less polite. It would be something like saying, “If I have to talk slower, you have to tell me.”
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Thank you Bruce, that was very helpful and feel like I understand this much more now, amazing how much a missing comma makes a difference.