just make sure your reputation with NCR is 'Liked' before you complete Side Bets, then you should be good.
To expand on this a bit:
Completion of
Wild Card: Side Bets will inflict a
large hit on your reputation with NCR and the Legion, and if it drops low enough they will refuse to work with you any further as they can no loner trust you. If you persist with the Yes Man route at this point they will start sending hit squads and will hate you for the remainder of the game.
The initial warning of this comes upon dealing with Mr. House during
Wild Card: Change in Management, when you are told that further dealings with Yes Man will turn NCR/Legion against you. You can still do
Side Bets without further penalty, however upon settling the last group's status (doesn't matter who this is) the rep hit will be inflicted even though you haven't reported it to Yes Man yet.
If your Reputation with the NCR is high enough (such as
'Liked', as mentioned above) they will not hate you outright for siding with Yes Man to this point, although it won't take much more to push them past the Point of No Return?.
Yes Man will never hate you, so you can then work the NRC route up to the point of choosing who to back during Second Hoover Dam. Choosing one of the two will block the option to work with the other (and backing YM will make the NCR despise you regardless of current reputation), so at that point you'll have to decide who to go with or even to not go any further (I often do the latter as I like being able to putter around for as long as I choose).