Yes, the residuals might be both positive and negative. The linear regression typically minimizes the square of them.
In case of two-dimensional input, we obtain a regression plane and the residuals are calculated in the same way.
EDIT: The regression plane is defined as $$ z_i =\beta_0+\beta_1x_{i} +\beta_2y_{i}+\epsilon_i $$ and the residual is for given parameters $\beta_0,\beta_1,\beta_2$ and given data record $(z_i,y_i,x_i)$ calculated as $$ \epsilon_i=z_i -(\beta_0+\beta_1x_{i} +\beta_2y_{i}) $$ Similarly also with higher dimensions.