The number one priority of freedmen during Reconstruction was survival. Although emancipation from slavery is thought of today as a very righteous act it did not account for the transition of people from forced servitude to freedom. As a result, historians are finding that from 1862-1870 approximately four million neglected freedmen died. Author Jim Downs' book Sick From Freedom describes how diseases like smallpox and cholera led to this unfortunate end for many newly freed African Americans. Downs also claims that it was Union soldiers that were the main culprit—they often failed to get sick freedmen the necessary medical help.
The second priority of freedmen was to reunite families and then, as you mentioned, create communities. Instead of going to white churches, African American places of worship were established for the first time. This was especially important because many Southerners were still bitter about the loss of family members and the war itself. Violence against freedmen by angry whites would start as early as 1865.
Reconstruction refers to the period of Southern Black Progress after the Civil War (~1860-1880), when the black community was accorded full citizenship (1866), right to vote, and other rights. The priorities developed during this time included building schools & churches, establishing towns, opening businesses, owning farmland, fighting to get equal rights (because there were still laws in place that restricted the lives of Black people), acquiring property and getting representation in the senate.
Emancipation refers to the presidential proclamation made by Lincoln in 1863 that set all the slaves free. It only included the states under the control of the Confederates and did not outlaw slavery. The immediate priorities of emancipation included getting the news as far out as possible to enable the freedom of as large a slave population as possible. Many freed slaves joined the Union army afterwards, while others (after reconstruction) left to gain employment or land for agriculture and slowly moved toward gaining a national identity as an important constituent of the US population.