That would work.Should I run a single 3/4 pex over the water heater and T the water heater supply line down to the water heater or do it differently?
They work. If you're using PEX there's no need to use Flex, use standard 3/4" rigid copper with a union and shutoff on the in and out side (so when you have to replace the hot water heater you will have an easy disconnect.) Check with your instructions and/or the PEX instructions to determine the distance from the water heater to PEX distance you must maintain...most I believe are 18".Second, should I use the flex copper connectors to and from the water heater?
Sure you can...but there are also many online sources that you may want to check into (price check the items you may be interested in...this site runs high). By the time you purchase the valves and T's you will have more into it than if you can find an online source. Plus a manifold will look much cleaner and reduces the number of connections by about 2/3.Runs are fairly short and I like the idea of using a hot and cold manifold with home runs to the fixtures. of course no manifolds are for sale around here. Can I make my own maifolds with PEX fittings and cutoffs of willa 3/4 manifold not supply enought pressure?
If you go with mainifolds, unless you have a high volume fill like a whirlpool tub, 1/2" will supply all you will need. If you go with out the manifold, sure, run 3/4" to the group, and split off with 1/2". Especially with the hot side....if you have a 3/4" pipe serving 3 fixtures in a manifold I will almost gaurantee you will be posting back wanting to know how to speed up the hot water delivery. If you have a run of decent length, there's many gallons of cold water to replace before the hot is available.
3/4" pipe will NOT increase or decrease pressure...it will affect volume.
Hope this get's you started...