Shop 3-way switches for two receptacles with 2 additional receptacles not controlled by the 3-way switches
Sure.  But it will take 5 wires, and due to the equal-current rules, you can't just gang a /2 and /3.  Given the goofy cable required, conduit makes more sense costwise. 

First, do you want the always-hot and switched-hot on separate circuits?  I do that so my dumb mistakes don't plunge me in the dark.

Receptacles come in white, beige, black, gray and if you hunt really hard you can find other colors.  Plan for different color receptacles for the lights vs the always-hot.

Also, because fitting wires onto screws from a ladder is a nightmare, I suggest you sit at an ergonomically comfortable workbench, and pigtail every single receptacle.   Yes, I know receptacles have 2 screws on each side and pigtailing isn't necessary. 

When I say "run a wire from source to each box. i mean daisy-chain: run source to box 1, box 1 to box 2, box 2 to box 3, etc. 

Method 1: conduit, one circuit, source anywhere

You will use a variety of wire colors, the purpose of which is to make this wiring job stupid-easy.   You can use fewer colors at your peril but if you do, I very strongly recommend getting a $3 pack of 5 colors of tape, and marking every wire  that isn't natively that color. Feel free to change my color code, just be consistent! 

Pigtail your to-be-always-on receptacles with black on the hot side and white on the neutral side.   Pigtail your lamp receptacles with red on the hot side and white on neutral.   


run 2 yellow messengers between the two 3-way switches. There is no need to distinguish these from each other.  These land on the two brass screws on both switches, leaving one screw left.  That was easy!  
A single black always-hot wire connecting supply to one of the 3-way switches and every receptacle location (where you want always-hot).
a single red switched-hot wire connecting the other 3-way switch and every receptacle location (where you want lamps). 
a single white neutral wire connecting supply to every receptacle location. 
grounds everywhere (EMT is ground)


Anywhere the wires need to stop to connect to something, you can cut, but leave 8" of slack on each end of each box.  The messengers pass thru and don't need a loop or slack in passthru boxes. 

Wiring the 3-ways is stupid easy because one wire at each switch is unaccounted for, and one black terminal remains.  

Nothing left but receptacles and it's all color coded.  Nut together all the white neutrals, black hots and red switched-hots. 

Method 2: conduit, two circuits, source anywhere

An even larger variety of colors, introducing brown and gray for the second circuit. 

Pigtail your to-be-always-on receptacles with black on the hot side and white on the neutral side.   Pigtail your lamp receptacles with brown on the hot side and gray on neutral.   


run 2 yellow wires for messengers between the 3-ways, and again they use up all the brass screws on the 3-ways.  
run a brown wire (lighting always-hot) from supply to one 3-way switch, only. 
run a red wire (lighting switched-hot) between the other 3-way and every lighting receptacle. 
run a gray wire (lighting neutral) between supply and every lamp receptacle location. 
run a black wire (service hot) and white wire (service neutral) between supply and every service receptacle location. 
grounds everywhere (EMT is ground) 


Spare wire to the black screw  on the 3-ways as before, then join same colors.  Done.

With flexible cable (one circuit)

Just to put you on notice, this will be a nightmare tangle. As you may have gathered, you cannot do this with a single cable unless you have a source for /5 cable.   But also, there are current-return rules that must be followed.  

You will need to tape wires colors, or you will lose your mind.  Upside, you only need one color of tape. When you mark a wire, mark both ends at once.  

Fasten your seat belt!

Sit at your ergonomic workstation, and pigtail all the always-hot receptacles with black and white, and the switched-hot receptacles with red and white.  

From supply, run a /4 cable (you heard me) to 3-way switch #1.  On this cable, tag the red and blue wires with yellow tape.  

From supply, run a /4 cable to the other 3-way.  On this cable, tag the black and blue wires with yellow tape.  

Between supply and each of the receptacle locations, run /3 cable.  Yes, this may involve paralleling the /4 cable.  This is necessary due to current balance rules.  

At each 3-way:  yellow is messengers and you land them on both brass screws on the 3-way.   White is neutral and is unused, for now.  The remaining wire goes on the black screw. 

At source (if it isn't a 3-way box): nut the 2 yellows "thru" the box.

Now join all blacks to blacks, reds to reds, whites to whites.  Done. 

If you can't get /4 cable you are allowed to use /2/2 cable and use the white-red in place of blue. Taping it yellow will mark it as a hot.  

With flexible cable (2 circuits)

Fuggedaboutit. 

No seriously it can be done, but you use /2/2 cable (not /4) between supply and each receptacle, and to the 3-ways. 

Follow the above instructons with a few changes. 


lighting receptacles get pigtailed with red and red-white-stripe
service receptacles get pigtailed with black and white (or white-black-stripe)
/2/2 cable has a white-striped-red wire instead of a blue. That becomes lighting circuit neutral. 
brown is lighting-circuit supply hot.  
on the /2/2's to the 3-ways, tape the black and white (or white-striped-black) wires yellow. 
on the /2/2 cable to 3-way #1, tape the red wire brown, "lighting circuit supply always-hot".


Now your color codes are 


black - always-hot (service circuit)
white or white-striped-black - neutral (service circuit)
brown - always-hot (lighting circuit)
white-striped-red - neutral (lighting circuit)
red - switched-hot (lighting circuit)
yellow - messengers


Join 'em.