Settlements are encouraged in almost all cases filed either in courts of law or..as in your case...quasi-judicial agency NLRC.
It ends, albeit settle for good, a rather long and grinding process of litigation.
However before you enter into an amicable settlement ask first if what your adverse party is offering is acceptable, favorable and satisfactory to you. If so then yes it is OK to enter into an amicable settlement.
All amicable settlement will undergo the scrutiny of the judge or arbiter where the case is settled. The judge or arbiter will ask you if the amicable settlement being offered acceptable on your part...if so he will make an order giving approval of the amicable settlement of the case you filed. Ergo by virtue of the amicable settlement, the dispute which gave rise to the filing of the case has been settled hence there is no point in continuing to proceed the case based on its merits and as a natural course...the case you filed will be dismissed since, to reiterate, the amicable settlement already settled your dispute with your adverse party
I see no reason why settlements will have a negative impact on your future employment since most cases filed in the NLRC are not publicized. unless companies will take time to research on the people filing cases in the NLRC..which we all know goes by the hundreds if not by the thousand each day in a given work week...I think not even multinational companies will devout so much time doing this.
Good luck and God speed..I hope I was able to give answers to your question. Thank you!